Biowerkzeug Wiki biowerkzeug https://biowerkzeug.org/index.php?title=Main_Page MediaWiki 1.43.0 first-letter Media Special Talk User User talk Biowerkzeug Wiki Biowerkzeug Wiki talk File File talk MediaWiki MediaWiki talk Template Template talk Help Help talk Category Category talk 0 1 1 2008-06-03T13:13:39Z MediaWiki default 0 wikitext text/x-wiki <big>'''MediaWiki has been successfully installed.'''</big> Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software. == Getting started == * [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list] * [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ] * [http://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list] 08fc850f2898611c250d639e30f69532b5a016f8 2 1 2008-06-03T15:29:37Z 129.67.76.50 0 /* Getting started */ wikitext text/x-wiki <big>'''MediaWiki has been successfully installed.'''</big> Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software. This Wiki discusses biomolecular simulations with [[Hippo]] and other molecular dynamics/Monte Carlo codes. It serves as a repository for the community and complements the [http://forums.biowerkzeug.org forums]. == Getting started == * [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list] * [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ] * [http://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list] 503a5d428bb7dd86ce332e0f2a4a2986a3775f70 3 2 2008-06-03T15:30:19Z 129.67.76.50 0 wikitext text/x-wiki This Wiki discusses biomolecular simulations with [[Hippo]] and other molecular dynamics/Monte Carlo codes. It serves as a repository for the community and complements the [http://forums.biowerkzeug.org forums]. == Getting started == * [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] * [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list] * [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ] * [http://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list] aabf55cb630270621420f93e4bceda1bcc185f36 4 3 2008-06-13T15:47:49Z Alexander 4 wikitext text/x-wiki This Wiki discusses biomolecular simulations with [[Hippo]] and other molecular dynamics/Monte Carlo codes. It serves as a repository for the community and complements the [http://forums.biowerkzeug.org forums]. Source Code Test: <source lang="php"> <?php $v = "string"; // sample initialization ?> html text <? echo $v; // end of php code ?> </source> == Getting started == * [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] * [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list] * [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ] * [http://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list] a5a9c1481f629b015b86d36bccd8c98302c51bf4 5 4 2008-06-13T15:48:03Z Alexander 4 wikitext text/x-wiki This Wiki discusses biomolecular simulations with [[Hippo]] and other molecular dynamics/Monte Carlo codes. It serves as a repository for the community and complements the [http://forums.biowerkzeug.org forums]. == Getting started == * [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] * [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list] * [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ] * [http://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list] aabf55cb630270621420f93e4bceda1bcc185f36 6 5 2008-06-27T20:52:44Z Oliver 2 basic layout wikitext text/x-wiki This Wiki discusses biomolecular simulations with [[Hippo]] and other molecular dynamics/Monte Carlo codes. It serves as a repository for the community and complements the [http://forums.biowerkzeug.org forums]. == Overview == * [[Molecular dynamics]] * [[Monte Carlo]] * [[Force fields]] * [[Algorithms]] * [[Solvents]] * [[Membranes]] == Getting started == * [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] * [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list] * [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ] * [http://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list] ab15cf8c5e54afab91d4b210dd578ab1bcb71732 8 6 2008-06-27T21:09:17Z Oliver 2 formatting: double columned (see de.wikipedia.org main page); still nedd css wikitext text/x-wiki {| width="100%" cellspacing="0" cellpadding="0" | colspan="2" | This Wiki discusses biomolecular simulations with [[Hippo]] and other molecular dynamics/Monte Carlo codes. It serves as a repository for the community and complements the [http://forums.biowerkzeug.org forums]. |- | width="50%" style="vertical-align:top;" | == Overview == * [[Molecular dynamics]] * [[Monte Carlo]] * [[Force fields]] * [[Algorithms]] * [[Solvents]] * [[Membranes]] | width="50%" style="vertical-align:top;" | == Getting started == * [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] * [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list] * [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ] * [http://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list] |} 8edaaac765f1d4d43d94f1efa489ee1a7475ed12 16 8 2008-06-27T23:37:28Z Martin 5 added hippo section wikitext text/x-wiki {| width="100%" cellspacing="0" cellpadding="0" | colspan="2" | This Wiki discusses biomolecular simulations with [[Hippo]] and other molecular dynamics/Monte Carlo codes. It serves as a repository for the community and complements the [http://forums.biowerkzeug.org forums]. |- | width="50%" style="vertical-align:top;" | == Molecular Mechanics == * [[Molecular dynamics]] * [[Monte Carlo]] * [[Force fields]] * [[Algorithms]] * [[Solvents]] * [[Membranes]] | width="50%" style="vertical-align:top;" | == Hippo == * [[Simulations]] * [[Analysis]] * [[Graphical interface]] * [[Files and features]] |- | width="50%" style="vertical-align:top;" | == Getting started == * [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] * [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list] * [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ] * [http://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list] |} 5ecf4e74d0729decec70dd259d92c8c2676d438a 17 16 2008-06-29T12:29:00Z Mrtest 6 /* Molecular Mechanics */ wikitext text/x-wiki {| width="100%" cellspacing="0" cellpadding="0" | colspan="2" | This Wiki discusses biomolecular simulations with [[Hippo]] and other molecular dynamics/Monte Carlo codes. It serves as a repository for the community and complements the [http://forums.biowerkzeug.org forums]. |- | width="50%" style="vertical-align:top;" | <div class="inhalt"> == Molecular Mechanics == * [[Molecular dynamics]] * [[Monte Carlo]] * [[Force fields]] * [[Algorithms]] * [[Solvents]] * [[Membranes]] </div> | width="50%" style="vertical-align:top;" | == Hippo == * [[Simulations]] * [[Analysis]] * [[Graphical interface]] * [[Files and features]] |- | width="50%" style="vertical-align:top;" | == Getting started == * [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] * [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list] * [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ] * [http://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list] |} a782a284c5efb1108eebaaafba2d4c406048ad1a 18 17 2008-06-29T12:29:15Z Mrtest 6 /* Molecular Mechanics */ wikitext text/x-wiki {| width="100%" cellspacing="0" cellpadding="0" | colspan="2" | This Wiki discusses biomolecular simulations with [[Hippo]] and other molecular dynamics/Monte Carlo codes. It serves as a repository for the community and complements the [http://forums.biowerkzeug.org forums]. |- | width="50%" style="vertical-align:top;" | <div class="inhalt"> == Molecular Mechanics == * [[Molecular dynamics]] * [[Monte Carlo]] * [[Force fields]] * [[Algorithms]] * [[Solvents]] * [[Membranes]] | width="50%" style="vertical-align:top;" | == Hippo == * [[Simulations]] * [[Analysis]] * [[Graphical interface]] * [[Files and features]] |- | width="50%" style="vertical-align:top;" | == Getting started == * [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] * [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list] * [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ] * [http://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list] |} a70ad08ce513bbfbf21e1a5b5977dc5bfb1fbda8 19 18 2008-06-29T16:38:11Z Oliver 2 renamed 'Molec Mechanics' --> 'Molec simulations'; added box for Visualization wikitext text/x-wiki {| width="100%" cellspacing="0" cellpadding="0" | colspan="2" | This Wiki discusses biomolecular simulations with [[Hippo]] and other molecular dynamics/Monte Carlo codes. It serves as a repository for the community and complements the [http://forums.biowerkzeug.org forums]. |- | width="50%" style="vertical-align:top;" | <div class="inhalt"> == Molecular simulations == * [[Molecular dynamics]] * [[Monte Carlo]] * [[Force fields]] * [[Algorithms]] * [[Solvents]] * [[Membranes]] | width="50%" style="vertical-align:top;" | == Hippo == * [[Simulations]] * [[Analysis]] * [[Graphical interface]] * [[Files and features]] == Visualization == * [[Visualization software]] * Visualization [[Visualization tutorial|tutorial]] with [[VMD]] * [[Movie tutorial]] |- | width="50%" style="vertical-align:top;" | == Getting started == * [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] * [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list] * [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ] * [http://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list] |} c66be9774c60eeb74c93d765aaa21796af138896 20 19 2008-06-29T16:54:41Z Oliver 2 ground rules; MediaWiki links will be moved to Edit help wikitext text/x-wiki __NOTOC__ {| width="100%" cellspacing="0" cellpadding="0" | colspan="2" | This Wiki discusses biomolecular simulations with [[Hippo]] and other molecular dynamics/Monte Carlo codes. It serves as a repository for the community and complements the [http://forums.biowerkzeug.org forums]. Please contribute your own knowledge to this Wiki: If anything is unclear and you know how to write it better – change it. If you have useful tips & tricks – share them with everyone else. If you have comments on any article in this Wiki – start a discussion on the ''discussion'' page that accompanies every article (look in the top menu bar). We only ask you to [[Special:Userlogin|register]] when you edit pages. See [[Help:Editing|Help&rarr;Editing]] to get started on contributing to this community resource. |- | width="50%" style="vertical-align:top;" | <div class="inhalt"> == Molecular simulations == * [[Molecular dynamics]] * [[Monte Carlo]] * [[Force fields]] * [[Algorithms]] * [[Solvents]] * [[Membranes]] | width="50%" style="vertical-align:top;" | == Hippo == * [[Simulations]] * [[Analysis]] * [[Graphical interface]] * [[Files and features]] == Visualization == * Visualization [[Visualization software|software]] * Visualization [[Visualization tutorial|tutorial]] with [[VMD]] * [[Movie tutorial]] <!-- |- | width="50%" style="vertical-align:top;" | new section comes here --> |} 81f02db191d2518305f0529905f2a8d8f72c5605 22 20 2008-06-29T17:43:01Z Oliver 2 relabeling, reshuffling (Hippo should be first) wikitext text/x-wiki __NOTOC__ {| width="100%" cellspacing="0" cellpadding="0" | colspan="2" | This Wiki discusses biomolecular simulations with [[Hippo]] and other molecular dynamics/Monte Carlo codes. It serves as a repository for the community and complements the [http://forums.biowerkzeug.org forums]. Please contribute your own knowledge to this Wiki: If anything is unclear and you know how to write it better – change it. If you have useful tips & tricks – share them with everyone else. If you have comments on any article in this Wiki – start a discussion on the ''discussion'' page that accompanies every article (look in the top menu bar). We only ask you to [[Special:Userlogin|register]] when you edit pages. See [[Help:Editing|Help&rarr;Editing]] to get started on contributing to this community resource. |- | width="50%" style="vertical-align:top;" | == Hippo == * [[Simulations]] * [[Analysis]] * [[Graphical interface]] * [[Files and features]] == Methods == * [[Molecular dynamics]] * [[Monte Carlo]] * [[Force fields]] * [[Algorithms]] * [[Solvents]] * [[Membranes]] | width="50%" style="vertical-align:top;" | == Simulation protocols == * [[Globular proteins]] in solvent * [[Membrane proteins]] in membrane and solvent * [[Free energy calculations]] * [[Transition path sampling]] == Visualization == * Visualization [[Visualization software|software]] * Visualization [[Visualization tutorial|tutorial]] with [[VMD]] * [[Movie tutorial]] <!-- |- | width="50%" style="vertical-align:top;" | new section comes here --> |} c8443e90480dfdd19dcbfa14ce9986dbe3d74610 24 22 2008-06-29T18:05:49Z Oliver 2 use de wikipedia style sheet for boxes wikitext text/x-wiki <div id="hauptseite"> {| width="100%" cellspacing="0" cellpadding="0" | colspan="2" | This Wiki discusses biomolecular simulations with [[Hippo]] and other molecular dynamics/Monte Carlo codes. It serves as a repository for the community and complements the [http://forums.biowerkzeug.org forums]. Please contribute your own knowledge to this Wiki: If anything is unclear and you know how to write it better – change it. If you have useful tips & tricks – share them with everyone else. If you have comments on any article in this Wiki – start a discussion on the ''discussion'' page that accompanies every article (look in the top menu bar). We only ask you to [[Special:Userlogin|register]] when you edit pages. See [[Help:Editing|Help&rarr;Editing]] to get started on contributing to this community resource. |- | width="50%" style="vertical-align:top;" | <div class="hauptseite-links"> == Hippo == <div class="inhalt"> * [[Simulations]] * [[Analysis]] * [[Graphical interface]] * [[Files and features]] </div> == Methods == <div class="inhalt"> * [[Molecular dynamics]] * [[Monte Carlo]] * [[Force fields]] * [[Algorithms]] * [[Solvents]] * [[Membranes]] </div> </div> | width="50%" style="vertical-align:top;" | <div class="hauptseite-rechts"> == Simulation protocols == <div class="inhalt"> * [[Globular proteins]] in solvent * [[Membrane proteins]] in membrane and solvent * [[Free energy calculations]] * [[Transition path sampling]] </div> == Visualization == <div class="inhalt"> * Visualization [[Visualization software|software]] * Visualization [[Visualization tutorial|tutorial]] with [[VMD]] * [[Movie tutorial]] </div> </div> |} </div> __NOTOC__ e5dde77127fb6c0366c82958b3d9a222951fb49c 28 24 2008-06-29T21:21:23Z Oliver 2 formatting: put each section into its own div id="xxx" class="hauptseite-LINKS/RECHTS" wikitext text/x-wiki <div id="hauptseite"> {| width="100%" cellspacing="0" cellpadding="0" | colspan="2" | This Wiki discusses biomolecular simulations with [[Hippo]] and other molecular dynamics/Monte Carlo codes. It serves as a repository for the community and complements the [http://forums.biowerkzeug.org forums]. Please contribute your own knowledge to this Wiki: If anything is unclear and you know how to write it better – change it. If you have useful tips & tricks – share them with everyone else. If you have comments on any article in this Wiki – start a discussion on the ''discussion'' page that accompanies every article (look in the top menu bar). We only ask you to [[Special:Userlogin|register]] when you edit pages. See [[Help:Editing|Help&rarr;Editing]] to get started on contributing to this community resource. |- | width="50%" style="vertical-align:top;" | <div id="Hippo" class="hauptseite-links"> == Hippo == <div class="inhalt"> * [[Simulations]] * [[Analysis]] * [[Graphical interface]] * [[Files and features]] </div> </div> <div id="Methods" class="hauptseite-links"> == Methods == <div class="inhalt"> * [[Molecular dynamics]] * [[Monte Carlo]] * [[Force fields]] * [[Algorithms]] * [[Solvents]] * [[Membranes]] </div> </div> | width="50%" style="vertical-align:top;" | <div id="Simulation protocols" class="hauptseite-rechts"> == Simulation protocols == <div class="inhalt"> * [[Globular proteins]] in solvent * [[Membrane proteins]] in membrane and solvent * [[Free energy calculations]] * [[Transition path sampling]] </div> </div> <div id="Visualization" class="hauptseite-rechts"> == Visualization == <div class="inhalt"> * Visualization [[Visualization software|software]] * Visualization [[Visualization tutorial|tutorial]] with [[VMD]] * [[Movie tutorial]] </div> </div> |} </div> __NOTOC__ ba3ac8445342f55c9eb21b99d18985a77d6849fc 29 28 2008-06-29T21:26:17Z Oliver 2 /* Software */ new section wikitext text/x-wiki <div id="hauptseite"> {| width="100%" cellspacing="0" cellpadding="0" | colspan="2" | This Wiki discusses biomolecular simulations with [[Hippo]] and other molecular dynamics/Monte Carlo codes. It serves as a repository for the community and complements the [http://forums.biowerkzeug.org forums]. Please contribute your own knowledge to this Wiki: If anything is unclear and you know how to write it better – change it. If you have useful tips & tricks – share them with everyone else. If you have comments on any article in this Wiki – start a discussion on the ''discussion'' page that accompanies every article (look in the top menu bar). We only ask you to [[Special:Userlogin|register]] when you edit pages. See [[Help:Editing|Help&rarr;Editing]] to get started on contributing to this community resource. |- | width="50%" style="vertical-align:top;" | <div id="Hippo" class="hauptseite-links"> == Hippo == <div class="inhalt"> * [[Simulations]] * [[Analysis]] * [[Graphical interface]] * [[Files and features]] </div> </div> <div id="Methods" class="hauptseite-links"> == Methods == <div class="inhalt"> * [[Molecular dynamics]] * [[Monte Carlo]] * [[Force fields]] * [[Algorithms]] * [[Solvents]] * [[Membranes]] </div> </div> | width="50%" style="vertical-align:top;" | <div id="Simulation protocols" class="hauptseite-rechts"> == Simulation protocols == <div class="inhalt"> * [[Globular proteins]] in solvent * [[Membrane proteins]] in membrane and solvent * [[Free energy calculations]] * [[Transition path sampling]] </div> </div> <div id="Visualization" class="hauptseite-rechts"> == Visualization == <div class="inhalt"> * Visualization [[Visualization software|software]] * Visualization [[Visualization tutorial|tutorial]] with [[VMD]] * [[Movie tutorial]] </div> </div> <div id="Software" class="hauptseite-rechts"> == Software == <div class="inhalt"> * [[Molecular dynamics codes]] * [[Monte Carlo codes]] * [[Electrostatics]] and [[Brownian dynamics]] * [[Analysis software]] </div> </div> |} </div> __NOTOC__ f6de1b523966ac615078a4209127d39264b9b5e0 48 29 2008-06-30T14:55:43Z Oliver 2 /* Software */ model building and visualization wikitext text/x-wiki <div id="hauptseite"> {| width="100%" cellspacing="0" cellpadding="0" | colspan="2" | This Wiki discusses biomolecular simulations with [[Hippo]] and other molecular dynamics/Monte Carlo codes. It serves as a repository for the community and complements the [http://forums.biowerkzeug.org forums]. Please contribute your own knowledge to this Wiki: If anything is unclear and you know how to write it better – change it. If you have useful tips & tricks – share them with everyone else. If you have comments on any article in this Wiki – start a discussion on the ''discussion'' page that accompanies every article (look in the top menu bar). We only ask you to [[Special:Userlogin|register]] when you edit pages. See [[Help:Editing|Help&rarr;Editing]] to get started on contributing to this community resource. |- | width="50%" style="vertical-align:top;" | <div id="Hippo" class="hauptseite-links"> == Hippo == <div class="inhalt"> * [[Simulations]] * [[Analysis]] * [[Graphical interface]] * [[Files and features]] </div> </div> <div id="Methods" class="hauptseite-links"> == Methods == <div class="inhalt"> * [[Molecular dynamics]] * [[Monte Carlo]] * [[Force fields]] * [[Algorithms]] * [[Solvents]] * [[Membranes]] </div> </div> | width="50%" style="vertical-align:top;" | <div id="Simulation protocols" class="hauptseite-rechts"> == Simulation protocols == <div class="inhalt"> * [[Globular proteins]] in solvent * [[Membrane proteins]] in membrane and solvent * [[Free energy calculations]] * [[Transition path sampling]] </div> </div> <div id="Visualization" class="hauptseite-rechts"> == Visualization == <div class="inhalt"> * Visualization [[Visualization software|software]] * Visualization [[Visualization tutorial|tutorial]] with [[VMD]] * [[Movie tutorial]] </div> </div> <div id="Software" class="hauptseite-rechts"> == Software == <div class="inhalt"> * [[Molecular dynamics codes]] * [[Monte Carlo codes]] * [[Electrostatics]] and [[Brownian dynamics]] * [[Model building]] * [[Visualization software|Visualization]] * [[Analysis software]] </div> </div> |} </div> __NOTOC__ 1e22b190240290b5a86e86c75380ee3d638841a0 0 2 7 2008-06-27T20:57:27Z Oliver 2 basic structure wikitext text/x-wiki This section discusses various solvent models that can be used in molecular simulations. Generally speaking, there is a trade-off between detailed description and computational speed to be made. Depending on the problem, one or the other may be more important. This page may help you to make this decision. = Explicit solvent = == Three-site models == * [[TIP3P]] * [[SPC]] and [[SPC/E]] == Four-site models == * [[TIP4P]] == Five-site models == * [[TIP5P]] = Implicit solvent = == Poisson-Boltzmann == == Generalized Born == == Constant dielectric == b2ca4a45d1ccb6b30c7eabcdb08202efa2be61b8 10 7 2008-06-27T21:27:35Z Oliver 2 wikitext text/x-wiki This section discusses various solvent models that can be used in molecular simulations. Generally speaking, there is a trade-off between detailed description and computational speed to be made. Depending on the problem, one or the other may be more important. This page may help you to make this decision. = Explicit solvent = == Three-site models == * [[TIP3P]] * [[SPC]] and [[SPC/E]] == Four-site models == * [[TIP4P]] == Five-site models == * [[TIP5P]] = Implicit solvent = == Poisson-Boltzmann == == Generalized Born == == Constant dielectric == {{Category:Solvents}} a0729be1d0d1b4f038bd4896b9fdeb7be86d682a 12 10 2008-06-27T21:29:34Z Oliver 2 wikitext text/x-wiki This section discusses various solvent models that can be used in molecular simulations. Generally speaking, there is a trade-off between detailed description and computational speed to be made. Depending on the problem, one or the other may be more important. This page may help you to make this decision. = Explicit solvent = == Three-site models == * [[TIP3P]] * [[SPC]] and [[SPC/E]] == Four-site models == * [[TIP4P]] == Five-site models == * [[TIP5P]] = Implicit solvent = == Poisson-Boltzmann == == Generalized Born == == Constant dielectric == [[Category:Solvents]] 67beac681b275b5a001ea6319da71320342f7f6f 0 3 9 2008-06-27T21:24:43Z Oliver 2 basic layout wikitext text/x-wiki Simulating the motion of molecules by iteratively solving Newton's equation of motion. = Integrators = * [[Verlet]] * [[Velocity Verlet]] 43ae26e17d24ee6f6c5d6a29e13e3a4dee846945 14 4 11 2008-06-27T21:28:21Z Oliver 2 stub wikitext text/x-wiki Solvents contains pages that deal with the question how the solvent (typically water and ions) are represented. 73774c6998e9752b3d6ecec070ba602bddc5528a 0 5 13 2008-06-27T21:44:54Z Oliver 2 basic layout + testing of biblio (it works! yay!) wikitext text/x-wiki Simulations of proteins must also represent the environment faithfully (simulations in [[vacuum simulations|vacuum]] are ''not'' appropriate in most cases and really date back to the days when computer resources were severely limited). The environment of a protein consists of the [[solvent]] and, if it's a membrane protein, of the [[lipid bilayer]]. Here we discuss methods to represent the '''lipid membrane'''. == Explicit lipids == === All atom === All atom representations include heavy atoms and ''all'' hydrogens. See [[#United atom|united atom]] for the alternative. === United atom === A ''united atom'' representation combines carbons and aliphatic hydrogens into ''unified'' particles. == Implicit membrane == === Dielectric slab === === Statistical potential-based membrane === The membrane is parametrized based on the distribution of amino acids along the bilayer normal <cite>Ulmschneider2005</cite>. = References = <biblio> #Ulmschneider2005 pmid=15723347 </biblio> 98dbfd5d239562ea6988e6fff99417b4cc0493a8 14 13 2008-06-27T21:45:25Z Oliver 2 wikitext text/x-wiki Simulations of proteins must also represent the environment faithfully (simulations in [[vacuum simulations|vacuum]] are ''not'' appropriate in most cases and really date back to the days when computer resources were severely limited). The environment of a protein consists of the [[solvent]] and, if it's a membrane protein, of the [[lipid bilayer]]. Here we discuss methods to represent the '''lipid membrane'''. == Explicit lipids == === All atom === All atom representations include heavy atoms and ''all'' hydrogens. See [[#United atom|united atom]] for the alternative. === United atom === A ''united atom'' representation combines carbons and aliphatic hydrogens into ''unified'' particles. == Implicit membrane == === Dielectric slab === === Statistical potential-based membrane === The membrane is parametrized based on the distribution of amino acids along the bilayer normal <cite>Ulmschneider2005</cite>. == References == <biblio> #Ulmschneider2005 pmid=15723347 </biblio> 6e95b967fe73b3691df9893262f84436cafe88e4 0 6 15 2008-06-27T21:46:39Z Oliver 2 Redirecting to [[Solvents]] wikitext text/x-wiki #REDIRECT [[Solvents]] d40db36c26d0177d95b318a6af8eca8e48360c1e 12 7 21 2008-06-29T16:55:37Z Oliver 2 copied Help page from Woolflab wiki wikitext text/x-wiki This page should tell you how to work with this Wiki &ndash; it's not complicated, promise! (In fact, the whole point of a wiki is to make it as easy for the user as possible to document whatever there is worth documenting). ==Editing an existing page== # Select the ''Edit'' link at the top. # Type or simply copy and paste text, eg from your editor, shell, or an email, and use the ''preview'' button. # Once it looks sort-of right commit your changes by clicking ''save page''. The Media Wiki page has a comprehensive list of the [http://meta.wikipedia.org/wiki/MediaWiki_User%27s_Guide:_Editing_overview#The_wiki_markup Wiki markup] but you can also look at the code of existing pages (edit the page but don't save it) or use the formatting buttons at the top of your editing box. The most important thing is just to put something on the page and not to worry too much about formatting. If in doubt simply leave one initial space and everything gets formatted verbatim; anything resembling an URL will be turned into a link (or enclose it in <nowiki>'[' and ']'</nowiki>). ==Editing a new page== If you click on a red link then you enter a non-existing page. This is not bad: Simply start editing it and ''write it yourself''. You can't make mistakes. Just do it. ==Creating a new page== To make a non-existing page you simply insert the link into an existing page, it appears in red, you click it and then edit it. == Signing your name == Sometimes this is useful: three tildes <nowiki>~~~</nowiki> signs your name like this: [[User:Oliver|Oliver]]; four <nowiki>~~~~</nowiki> dates it too: [[User:Oliver|Oliver]] 18:32, 24 January 2006 (EST) ==Categories== [http://meta.wikimedia.org/wiki/Help:Category '''Categories''' in MediaWiki] provide automatic indexes that are useful as tables of contents. See the Special Page '''[[Special:Categories]]''' for a list of all defined categories. You define a category by adding one or more special tags at the end of a page: add "<nowiki>[[</nowiki>Category:''Category name''<nowiki>]]</nowiki>" to the page's wikitext source. For instance, add to page that describes analysis scripts for Charmm <nowiki>[[Category:Charmm]]</nowiki> <nowiki>[[Category:Analysis]]</nowiki> as the last two lines. This will implicitly define the categories [[:Category:Analysis]] and [[:Category:Charmm]]. The category pages can also be edited. In addition, the wiki software adds an alphabetically sorted list of all pages in the category. This makes a category useful as an entry point into a subject. '''Note''': One ''must'' edit a category page for the wiki to create the indexed list (even if it is just an empty edit). In order to reference a category within a page as a normal wiki link (without adding the page to the category) prefix the link name with a colon. For example: <nowiki>[[:</nowiki>Category:Analysis<nowiki>]]</nowiki>. == Page maintenance == === Redirection === A 'symbolic link' to another pages is created with the [http://meta.wikimedia.org/wiki/Help:Redirection REDIRECT] command: <nowiki>#REDIRECT [[</nowiki>''page''<nowiki>]]</nowiki> ==Highlighting sourcecode== Wikimedia can do syntax highlighting for over a dozen programming languages, including c, python, perl, fortran, and c++. Just surround the code with a tag of the name of the language. For example: <pre> <python> import re lines = file("ifconf.log").readlines() l_iter = iter(lines) nodes = [] for l in l_iter: if l[:7] == "compute": node = l.split('.')[0] temp = l_iter.next().split() iface, addr = temp[0], temp[4] nodes.append([node, iface, addr]) </python> </pre> Gives you <python> import re lines = file("ifconf.log").readlines() l_iter = iter(lines) nodes = [] for l in l_iter: if l[:7] == "compute": node = l.split('.')[0] temp = l_iter.next().split() iface, addr = temp[0], temp[4] nodes.append([node, iface, addr]) </python> ==Inserting Gnuplot graphs== You can insert gnuplot graphs directly into mediawiki by using the <tt>gnuplot</tt> tag. For example: <pre> <gnuplot> set output 'func_approx.png' plot '-' using 1:2 t 'quadratic approximation' with linesp lt 1 lw 3, \ '-' using 1:2 t 'cubic approximation' with linesp lt 2 lw 3 1 2 2 4 3 8 4 16 e 1 3 2 9 3 27 4 81 e </gnuplot> </pre> Gives you the following: <gnuplot> set output 'func_approx.png' plot '-' using 1:2 t 'quadratic approximation' with linesp lt 1 lw 3, \ '-' using 1:2 t 'cubic approximation' with linesp lt 2 lw 3 1 2 2 4 3 8 4 16 e 1 3 2 9 3 27 4 81 e </gnuplot> == Adding bibliographic references (specifically [http://www.pubmed.gov PubMed]) == You can insert bibliographic references into pages by using the <tt><nowiki><cite></nowiki></tt> and <tt><nowiki><biblio></nowiki></tt> tags. This uses the PubMed id number (pmid) found at the bottom of the abstract listing for a particular article. Mediawiki will go to [http://www.pubmed.gov PubMed] and pull the citation information for the reference. Using the key in front of the pmid assignment within the <tt><nowiki><cite></nowiki></tt> tag (see example below) gives you a reference to the article within the current page. For example, although you can obmit the pmid and simply format the reference yourself. <pre> Recent papers from the Woolf lab <cite>jcp2005 proteins2005 jcp2004</cite>: ===Bibliography=== <biblio> #jcp2005 pmid=15847458 #proteins2005 pmid=15828005 #jcp2004 pmid=15634036 </biblio> </pre> Will give you this: Recent papers from the Woolf lab <cite>jcp2005 proteins2005 jcp2004</cite>: <b>Bibliography</b> <biblio> #jcp2005 pmid=15847458 #proteins2005 pmid=15828005 #jcp2004 pmid=15634036 </biblio> == Images == [[Image:NAChR M2 water.jpg|200px|right]] The following shows two methods of how to incorporate an image in a wiki page. === Upload === The image is uploaded to the webserver and resides in the wiki (somewhere... you don't need to know where, it's a secret) # first [[Special:Upload|upload]] it (use the link in the toolbox on the left) # enter a wiki link such as <tt><nowiki>[[Image:NAChR M2 water.jpg|200px]] </nowiki></tt> into the text An exhaustive description of the image capabilities are discussed in the [http://en.wikipedia.org/wiki/Wikipedia:Extended_image_syntax Wikipedia Extended Image Syntax]. Most importantly, if you want to change the size of the image, add a size option <tt>|''size''px</tt> option (<tt>|200px</tt> in the example above). The new version of MediaWiki gives you a plethora of options to add captions, float the image to left or right, change sizes, show it as a (fast) thumbnail, ... === Web link === Alternatively, just put in a link to a png or jpg such as <tt><nowiki>http://sbcb.bioch.ox.ac.uk/oliver/Priv/USA/California/goldenpoppy.png</nowiki></tt>: http://sbcb.bioch.ox.ac.uk/oliver/Priv/USA/California/goldenpoppy.png The image appears in its original size. == References == If you want to know more than what has been touched upon above, have a look at these links: * Wikipedia's [http://en.wikipedia.org/wiki/Wikipedia:How_to_edit_a_page full listing of wiki editing commands] (make sure you come back here to edit... otherwise you will be editing Wikipedia) * Wikipedia [http://en.wikipedia.org/wiki/Wikipedia:Extended_image_syntax Extended Image Syntax] for all your image inclusion needs * Syntax of [http://en.wikipedia.org/wiki/Help:Table Table] commands e8fe9945183698cdea454b5125fbdd34517e71e8 25 21 2008-06-29T20:47:37Z Oliver 2 /* Links */ moved MediaWiki to the Links section wikitext text/x-wiki This page should tell you how to work with this Wiki &ndash; it's not complicated, promise! (In fact, the whole point of a wiki is to make it as easy for the user as possible to document whatever there is worth documenting). ==Editing an existing page== # Select the ''Edit'' link at the top. # Type or simply copy and paste text, eg from your editor, shell, or an email, and use the ''preview'' button. # Once it looks sort-of right commit your changes by clicking ''save page''. The Media Wiki page has a comprehensive list of the [http://meta.wikipedia.org/wiki/MediaWiki_User%27s_Guide:_Editing_overview#The_wiki_markup Wiki markup] but you can also look at the code of existing pages (edit the page but don't save it) or use the formatting buttons at the top of your editing box. The most important thing is just to put something on the page and not to worry too much about formatting. If in doubt simply leave one initial space and everything gets formatted verbatim; anything resembling an URL will be turned into a link (or enclose it in <nowiki>'[' and ']'</nowiki>). ==Editing a new page== If you click on a red link then you enter a non-existing page. This is not bad: Simply start editing it and ''write it yourself''. You can't make mistakes. Just do it. ==Creating a new page== To make a non-existing page you simply insert the link into an existing page, it appears in red, you click it and then edit it. == Signing your name == Sometimes this is useful: three tildes <nowiki>~~~</nowiki> signs your name like this: [[User:Oliver|Oliver]]; four <nowiki>~~~~</nowiki> dates it too: [[User:Oliver|Oliver]] 18:32, 24 January 2006 (EST) ==Categories== [http://meta.wikimedia.org/wiki/Help:Category '''Categories''' in MediaWiki] provide automatic indexes that are useful as tables of contents. See the Special Page '''[[Special:Categories]]''' for a list of all defined categories. You define a category by adding one or more special tags at the end of a page: add "<nowiki>[[</nowiki>Category:''Category name''<nowiki>]]</nowiki>" to the page's wikitext source. For instance, add to page that describes analysis scripts for Charmm <nowiki>[[Category:Charmm]]</nowiki> <nowiki>[[Category:Analysis]]</nowiki> as the last two lines. This will implicitly define the categories [[:Category:Analysis]] and [[:Category:Charmm]]. The category pages can also be edited. In addition, the wiki software adds an alphabetically sorted list of all pages in the category. This makes a category useful as an entry point into a subject. '''Note''': One ''must'' edit a category page for the wiki to create the indexed list (even if it is just an empty edit). In order to reference a category within a page as a normal wiki link (without adding the page to the category) prefix the link name with a colon. For example: <nowiki>[[:</nowiki>Category:Analysis<nowiki>]]</nowiki>. == Page maintenance == === Redirection === A 'symbolic link' to another pages is created with the [http://meta.wikimedia.org/wiki/Help:Redirection REDIRECT] command: <nowiki>#REDIRECT [[</nowiki>''page''<nowiki>]]</nowiki> ==Highlighting sourcecode== Wikimedia can do syntax highlighting for over a dozen programming languages, including c, python, perl, fortran, and c++. Just surround the code with a tag of the name of the language. For example: <pre> <python> import re lines = file("ifconf.log").readlines() l_iter = iter(lines) nodes = [] for l in l_iter: if l[:7] == "compute": node = l.split('.')[0] temp = l_iter.next().split() iface, addr = temp[0], temp[4] nodes.append([node, iface, addr]) </python> </pre> Gives you <python> import re lines = file("ifconf.log").readlines() l_iter = iter(lines) nodes = [] for l in l_iter: if l[:7] == "compute": node = l.split('.')[0] temp = l_iter.next().split() iface, addr = temp[0], temp[4] nodes.append([node, iface, addr]) </python> ==Inserting Gnuplot graphs== You can insert gnuplot graphs directly into mediawiki by using the <tt>gnuplot</tt> tag. For example: <pre> <gnuplot> set output 'func_approx.png' plot '-' using 1:2 t 'quadratic approximation' with linesp lt 1 lw 3, \ '-' using 1:2 t 'cubic approximation' with linesp lt 2 lw 3 1 2 2 4 3 8 4 16 e 1 3 2 9 3 27 4 81 e </gnuplot> </pre> Gives you the following: <gnuplot> set output 'func_approx.png' plot '-' using 1:2 t 'quadratic approximation' with linesp lt 1 lw 3, \ '-' using 1:2 t 'cubic approximation' with linesp lt 2 lw 3 1 2 2 4 3 8 4 16 e 1 3 2 9 3 27 4 81 e </gnuplot> == Adding bibliographic references (specifically [http://www.pubmed.gov PubMed]) == You can insert bibliographic references into pages by using the <tt><nowiki><cite></nowiki></tt> and <tt><nowiki><biblio></nowiki></tt> tags. This uses the PubMed id number (pmid) found at the bottom of the abstract listing for a particular article. Mediawiki will go to [http://www.pubmed.gov PubMed] and pull the citation information for the reference. Using the key in front of the pmid assignment within the <tt><nowiki><cite></nowiki></tt> tag (see example below) gives you a reference to the article within the current page. For example, although you can obmit the pmid and simply format the reference yourself. <pre> Recent papers from the Woolf lab <cite>jcp2005 proteins2005 jcp2004</cite>: ===Bibliography=== <biblio> #jcp2005 pmid=15847458 #proteins2005 pmid=15828005 #jcp2004 pmid=15634036 </biblio> </pre> Will give you this: Recent papers from the Woolf lab <cite>jcp2005 proteins2005 jcp2004</cite>: <b>Bibliography</b> <biblio> #jcp2005 pmid=15847458 #proteins2005 pmid=15828005 #jcp2004 pmid=15634036 </biblio> == Images == [[Image:NAChR M2 water.jpg|200px|right]] The following shows two methods of how to incorporate an image in a wiki page. === Upload === The image is uploaded to the webserver and resides in the wiki (somewhere... you don't need to know where, it's a secret) # first [[Special:Upload|upload]] it (use the link in the toolbox on the left) # enter a wiki link such as <tt><nowiki>[[Image:NAChR M2 water.jpg|200px]] </nowiki></tt> into the text An exhaustive description of the image capabilities are discussed in the [http://en.wikipedia.org/wiki/Wikipedia:Extended_image_syntax Wikipedia Extended Image Syntax]. Most importantly, if you want to change the size of the image, add a size option <tt>|''size''px</tt> option (<tt>|200px</tt> in the example above). The new version of MediaWiki gives you a plethora of options to add captions, float the image to left or right, change sizes, show it as a (fast) thumbnail, ... === Web link === Alternatively, just put in a link to a png or jpg such as <tt><nowiki>http://sbcb.bioch.ox.ac.uk/oliver/Priv/USA/California/goldenpoppy.png</nowiki></tt>: http://sbcb.bioch.ox.ac.uk/oliver/Priv/USA/California/goldenpoppy.png The image appears in its original size. == Links == If you want to know more than what has been touched upon above, have a look at these links: === Wikipedia edit help documents === * Wikipedia's [http://en.wikipedia.org/wiki/Wikipedia:How_to_edit_a_page full listing of wiki editing commands] (make sure you come back here to edit... otherwise you will be editing Wikipedia) * Wikipedia [http://en.wikipedia.org/wiki/Wikipedia:Extended_image_syntax Extended Image Syntax] for all your image inclusion needs * Syntax of [http://en.wikipedia.org/wiki/Help:Table Table] commands === MediaWiki documents === The [http://wiki.biowerkzeug.org/ Biowerkzeug Wiki] uses the [http://www.mediawiki.org/wiki MediaWiki] software. For more on MediaWiki see the following links: * [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] * [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list] * [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ] * [http://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list] a8e7e833cf3139c918a2afa90a268a623a482a78 27 25 2008-06-29T21:11:57Z Oliver 2 /* Links */ wikitext text/x-wiki This page should tell you how to work with this Wiki &ndash; it's not complicated, promise! (In fact, the whole point of a wiki is to make it as easy for the user as possible to document whatever there is worth documenting). ==Editing an existing page== # Select the ''Edit'' link at the top. # Type or simply copy and paste text, eg from your editor, shell, or an email, and use the ''preview'' button. # Once it looks sort-of right commit your changes by clicking ''save page''. The Media Wiki page has a comprehensive list of the [http://meta.wikipedia.org/wiki/MediaWiki_User%27s_Guide:_Editing_overview#The_wiki_markup Wiki markup] but you can also look at the code of existing pages (edit the page but don't save it) or use the formatting buttons at the top of your editing box. The most important thing is just to put something on the page and not to worry too much about formatting. If in doubt simply leave one initial space and everything gets formatted verbatim; anything resembling an URL will be turned into a link (or enclose it in <nowiki>'[' and ']'</nowiki>). ==Editing a new page== If you click on a red link then you enter a non-existing page. This is not bad: Simply start editing it and ''write it yourself''. You can't make mistakes. Just do it. ==Creating a new page== To make a non-existing page you simply insert the link into an existing page, it appears in red, you click it and then edit it. == Signing your name == Sometimes this is useful: three tildes <nowiki>~~~</nowiki> signs your name like this: [[User:Oliver|Oliver]]; four <nowiki>~~~~</nowiki> dates it too: [[User:Oliver|Oliver]] 18:32, 24 January 2006 (EST) ==Categories== [http://meta.wikimedia.org/wiki/Help:Category '''Categories''' in MediaWiki] provide automatic indexes that are useful as tables of contents. See the Special Page '''[[Special:Categories]]''' for a list of all defined categories. You define a category by adding one or more special tags at the end of a page: add "<nowiki>[[</nowiki>Category:''Category name''<nowiki>]]</nowiki>" to the page's wikitext source. For instance, add to page that describes analysis scripts for Charmm <nowiki>[[Category:Charmm]]</nowiki> <nowiki>[[Category:Analysis]]</nowiki> as the last two lines. This will implicitly define the categories [[:Category:Analysis]] and [[:Category:Charmm]]. The category pages can also be edited. In addition, the wiki software adds an alphabetically sorted list of all pages in the category. This makes a category useful as an entry point into a subject. '''Note''': One ''must'' edit a category page for the wiki to create the indexed list (even if it is just an empty edit). In order to reference a category within a page as a normal wiki link (without adding the page to the category) prefix the link name with a colon. For example: <nowiki>[[:</nowiki>Category:Analysis<nowiki>]]</nowiki>. == Page maintenance == === Redirection === A 'symbolic link' to another pages is created with the [http://meta.wikimedia.org/wiki/Help:Redirection REDIRECT] command: <nowiki>#REDIRECT [[</nowiki>''page''<nowiki>]]</nowiki> ==Highlighting sourcecode== Wikimedia can do syntax highlighting for over a dozen programming languages, including c, python, perl, fortran, and c++. Just surround the code with a tag of the name of the language. For example: <pre> <python> import re lines = file("ifconf.log").readlines() l_iter = iter(lines) nodes = [] for l in l_iter: if l[:7] == "compute": node = l.split('.')[0] temp = l_iter.next().split() iface, addr = temp[0], temp[4] nodes.append([node, iface, addr]) </python> </pre> Gives you <python> import re lines = file("ifconf.log").readlines() l_iter = iter(lines) nodes = [] for l in l_iter: if l[:7] == "compute": node = l.split('.')[0] temp = l_iter.next().split() iface, addr = temp[0], temp[4] nodes.append([node, iface, addr]) </python> ==Inserting Gnuplot graphs== You can insert gnuplot graphs directly into mediawiki by using the <tt>gnuplot</tt> tag. For example: <pre> <gnuplot> set output 'func_approx.png' plot '-' using 1:2 t 'quadratic approximation' with linesp lt 1 lw 3, \ '-' using 1:2 t 'cubic approximation' with linesp lt 2 lw 3 1 2 2 4 3 8 4 16 e 1 3 2 9 3 27 4 81 e </gnuplot> </pre> Gives you the following: <gnuplot> set output 'func_approx.png' plot '-' using 1:2 t 'quadratic approximation' with linesp lt 1 lw 3, \ '-' using 1:2 t 'cubic approximation' with linesp lt 2 lw 3 1 2 2 4 3 8 4 16 e 1 3 2 9 3 27 4 81 e </gnuplot> == Adding bibliographic references (specifically [http://www.pubmed.gov PubMed]) == You can insert bibliographic references into pages by using the <tt><nowiki><cite></nowiki></tt> and <tt><nowiki><biblio></nowiki></tt> tags. This uses the PubMed id number (pmid) found at the bottom of the abstract listing for a particular article. Mediawiki will go to [http://www.pubmed.gov PubMed] and pull the citation information for the reference. Using the key in front of the pmid assignment within the <tt><nowiki><cite></nowiki></tt> tag (see example below) gives you a reference to the article within the current page. For example, although you can obmit the pmid and simply format the reference yourself. <pre> Recent papers from the Woolf lab <cite>jcp2005 proteins2005 jcp2004</cite>: ===Bibliography=== <biblio> #jcp2005 pmid=15847458 #proteins2005 pmid=15828005 #jcp2004 pmid=15634036 </biblio> </pre> Will give you this: Recent papers from the Woolf lab <cite>jcp2005 proteins2005 jcp2004</cite>: <b>Bibliography</b> <biblio> #jcp2005 pmid=15847458 #proteins2005 pmid=15828005 #jcp2004 pmid=15634036 </biblio> == Images == [[Image:NAChR M2 water.jpg|200px|right]] The following shows two methods of how to incorporate an image in a wiki page. === Upload === The image is uploaded to the webserver and resides in the wiki (somewhere... you don't need to know where, it's a secret) # first [[Special:Upload|upload]] it (use the link in the toolbox on the left) # enter a wiki link such as <tt><nowiki>[[Image:NAChR M2 water.jpg|200px]] </nowiki></tt> into the text An exhaustive description of the image capabilities are discussed in the [http://en.wikipedia.org/wiki/Wikipedia:Extended_image_syntax Wikipedia Extended Image Syntax]. Most importantly, if you want to change the size of the image, add a size option <tt>|''size''px</tt> option (<tt>|200px</tt> in the example above). The new version of MediaWiki gives you a plethora of options to add captions, float the image to left or right, change sizes, show it as a (fast) thumbnail, ... === Web link === Alternatively, just put in a link to a png or jpg such as <tt><nowiki>http://sbcb.bioch.ox.ac.uk/oliver/Priv/USA/California/goldenpoppy.png</nowiki></tt>: http://sbcb.bioch.ox.ac.uk/oliver/Priv/USA/California/goldenpoppy.png The image appears in its original size. == Links == If you want to gain an in-depth knowledge of working with this Wiki then have a look at these links: === Wikipedia edit help documents === * Wikipedia's [http://en.wikipedia.org/wiki/Wikipedia:How_to_edit_a_page full listing of wiki editing commands] (make sure you come back here to edit... otherwise you will be editing Wikipedia) * Wikipedia [http://en.wikipedia.org/wiki/Wikipedia:Extended_image_syntax Extended Image Syntax] for all your image inclusion needs * Syntax of [http://en.wikipedia.org/wiki/Help:Table Table] commands === MediaWiki documents === The [http://wiki.biowerkzeug.org/ Biowerkzeug Wiki] uses the [http://www.mediawiki.org/wiki MediaWiki] software. For more on MediaWiki see the following links: * [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] * [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list] * [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ] * [http://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list] 154a54598eff4b495070ba50d382ef9f200d248b 34 27 2008-06-29T21:49:56Z Oliver 2 category help wikitext text/x-wiki This page should tell you how to work with this Wiki &ndash; it's not complicated, promise! (In fact, the whole point of a wiki is to make it as easy for the user as possible to document whatever there is worth documenting). ==Editing an existing page== # Select the ''Edit'' link at the top. # Type or simply copy and paste text, eg from your editor, shell, or an email, and use the ''preview'' button. # Once it looks sort-of right commit your changes by clicking ''save page''. The Media Wiki page has a comprehensive list of the [http://meta.wikipedia.org/wiki/MediaWiki_User%27s_Guide:_Editing_overview#The_wiki_markup Wiki markup] but you can also look at the code of existing pages (edit the page but don't save it) or use the formatting buttons at the top of your editing box. The most important thing is just to put something on the page and not to worry too much about formatting. If in doubt simply leave one initial space and everything gets formatted verbatim; anything resembling an URL will be turned into a link (or enclose it in <nowiki>'[' and ']'</nowiki>). ==Editing a new page== If you click on a red link then you enter a non-existing page. This is not bad: Simply start editing it and ''write it yourself''. You can't make mistakes. Just do it. ==Creating a new page== To make a non-existing page you simply insert the link into an existing page, it appears in red, you click it and then edit it. == Signing your name == Sometimes this is useful: three tildes <nowiki>~~~</nowiki> signs your name like this: [[User:Oliver|Oliver]]; four <nowiki>~~~~</nowiki> dates it too: [[User:Oliver|Oliver]] 18:32, 24 January 2006 (EST) ==Categories== [http://meta.wikimedia.org/wiki/Help:Category '''Categories''' in MediaWiki] provide automatic indexes that are useful as tables of contents. See the Special Page '''[[Special:Categories]]''' for a list of all defined categories. You define a category by adding one or more special tags at the end of a page: add "<nowiki>[[</nowiki>Category:''Category name''<nowiki>]]</nowiki>" to the page's wikitext source. For instance, add to page that describes analysis scripts for Charmm <nowiki>[[Category:Charmm]]</nowiki> <nowiki>[[Category:Analysis]]</nowiki> as the last two lines. This will implicitly define the categories [[:Category:Analysis]] and [[:Category:Charmm]]. The category pages can also be edited. In addition, the wiki software adds an alphabetically sorted list of all pages in the category. This makes a category useful as an entry point into a subject. '''Note''': One ''must'' edit a category page for the wiki to create the indexed list (even if it is just an empty edit). In order to reference a category within a page as a normal wiki link (without adding the page to the category) prefix the link name with a colon. For example: <nowiki>[[:</nowiki>Category:Analysis<nowiki>]]</nowiki>. == Page maintenance == === Redirection === A 'symbolic link' to another pages is created with the [http://meta.wikimedia.org/wiki/Help:Redirection REDIRECT] command: <nowiki>#REDIRECT [[</nowiki>''page''<nowiki>]]</nowiki> ==Highlighting sourcecode== Wikimedia can do syntax highlighting for over a dozen programming languages, including c, python, perl, fortran, and c++. Just surround the code with a tag of the name of the language. For example: <pre> <python> import re lines = file("ifconf.log").readlines() l_iter = iter(lines) nodes = [] for l in l_iter: if l[:7] == "compute": node = l.split('.')[0] temp = l_iter.next().split() iface, addr = temp[0], temp[4] nodes.append([node, iface, addr]) </python> </pre> Gives you <python> import re lines = file("ifconf.log").readlines() l_iter = iter(lines) nodes = [] for l in l_iter: if l[:7] == "compute": node = l.split('.')[0] temp = l_iter.next().split() iface, addr = temp[0], temp[4] nodes.append([node, iface, addr]) </python> ==Inserting Gnuplot graphs== You can insert gnuplot graphs directly into mediawiki by using the <tt>gnuplot</tt> tag. For example: <pre> <gnuplot> set output 'func_approx.png' plot '-' using 1:2 t 'quadratic approximation' with linesp lt 1 lw 3, \ '-' using 1:2 t 'cubic approximation' with linesp lt 2 lw 3 1 2 2 4 3 8 4 16 e 1 3 2 9 3 27 4 81 e </gnuplot> </pre> Gives you the following: <gnuplot> set output 'func_approx.png' plot '-' using 1:2 t 'quadratic approximation' with linesp lt 1 lw 3, \ '-' using 1:2 t 'cubic approximation' with linesp lt 2 lw 3 1 2 2 4 3 8 4 16 e 1 3 2 9 3 27 4 81 e </gnuplot> == Adding bibliographic references (specifically [http://www.pubmed.gov PubMed]) == You can insert bibliographic references into pages by using the <tt><nowiki><cite></nowiki></tt> and <tt><nowiki><biblio></nowiki></tt> tags. This uses the PubMed id number (pmid) found at the bottom of the abstract listing for a particular article. Mediawiki will go to [http://www.pubmed.gov PubMed] and pull the citation information for the reference. Using the key in front of the pmid assignment within the <tt><nowiki><cite></nowiki></tt> tag (see example below) gives you a reference to the article within the current page. For example, although you can obmit the pmid and simply format the reference yourself. <pre> Recent papers from the Woolf lab <cite>jcp2005 proteins2005 jcp2004</cite>: ===Bibliography=== <biblio> #jcp2005 pmid=15847458 #proteins2005 pmid=15828005 #jcp2004 pmid=15634036 </biblio> </pre> Will give you this: Recent papers from the Woolf lab <cite>jcp2005 proteins2005 jcp2004</cite>: <b>Bibliography</b> <biblio> #jcp2005 pmid=15847458 #proteins2005 pmid=15828005 #jcp2004 pmid=15634036 </biblio> == Images == [[Image:NAChR M2 water.jpg|200px|right]] The following shows two methods of how to incorporate an image in a wiki page. === Upload === The image is uploaded to the webserver and resides in the wiki (somewhere... you don't need to know where, it's a secret) # first [[Special:Upload|upload]] it (use the link in the toolbox on the left) # enter a wiki link such as <tt><nowiki>[[Image:NAChR M2 water.jpg|200px]] </nowiki></tt> into the text An exhaustive description of the image capabilities are discussed in the [http://en.wikipedia.org/wiki/Wikipedia:Extended_image_syntax Wikipedia Extended Image Syntax]. Most importantly, if you want to change the size of the image, add a size option <tt>|''size''px</tt> option (<tt>|200px</tt> in the example above). The new version of MediaWiki gives you a plethora of options to add captions, float the image to left or right, change sizes, show it as a (fast) thumbnail, ... === Web link === Alternatively, just put in a link to a png or jpg such as <tt><nowiki>http://sbcb.bioch.ox.ac.uk/oliver/Priv/USA/California/goldenpoppy.png</nowiki></tt>: http://sbcb.bioch.ox.ac.uk/oliver/Priv/USA/California/goldenpoppy.png The image appears in its original size. == Links == If you want to gain an in-depth knowledge of working with this Wiki then have a look at these links: === Wikipedia edit help documents === * Wikipedia's [http://en.wikipedia.org/wiki/Wikipedia:How_to_edit_a_page full listing of wiki editing commands] (make sure you come back here to edit... otherwise you will be editing Wikipedia) * Wikipedia [http://en.wikipedia.org/wiki/Wikipedia:Extended_image_syntax Extended Image Syntax] for all your image inclusion needs * Syntax of [http://en.wikipedia.org/wiki/Help:Table Table] commands === MediaWiki documents === The [http://wiki.biowerkzeug.org/ Biowerkzeug Wiki] uses the [http://www.mediawiki.org/wiki MediaWiki] software. For more on MediaWiki see the following links: * [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] * [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list] * [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ] * [http://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list] [[Category:Help]] 00992069c04e48a05ee69a7eb25fcd2e1d2006e4 8 8 23 2008-06-29T17:54:07Z Oliver 2 copied 'Hauptseite' css from http://de.wikipedia.org/wiki/MediaWiki:Common.css css text/css /* CSS placed here will be applied to all skins */ /* Copied from http://de.wikipedia.org/wiki/MediaWiki:Common.css : "+++++ 3. NEUE [[Hauptseite|HAUPTSEITE]] (ab 2006) +++++" */ /* Kategorie verbergen */ body.page-Hauptseite #catlinks { display:none; } #hauptseite h2 { background-color: #d8e8ff; border: 1px solid #8898bf; font-size: 1em; font-weight: bold; margin-top: 0; margin-bottom: 0; padding-top: 0.1em; padding-bottom: 0.1em; } #hauptseite .inhalt { background-color: #ffffff; border: 1px solid #8898bf; border-top: 0px solid white; padding: 0.3em 0.8em 0.4em 0.8em; } #hauptseite .inhalt hr { background-color: #8898bf; color: #8898bf; height: 1px; margin:0.5em 0; padding: 0; } #hauptseite .inhalt .mehr { clear: both; font-size: 95%; margin-top: 0.8em; text-align: right; } .hauptseite-oben, .hauptseite-links, .hauptseite-rechts { margin-bottom: 1em; } .hauptseite-links { margin-right: 0.5em; } .hauptseite-rechts { margin-left: 0.5em; } .hauptseite-oben h2, .hauptseite-unten h2 { text-align: center; } .hauptseite-oben .inhalt .portale { font-weight: bold; margin-top: 0.2em; margin-bottom: 0.2em; } .hauptseite-oben .inhalt .intern { font-size: 90%; text-align: center; } .hauptseite-links h2, .hauptseite-rechts h2 { text-indent: 0.8em; } #hauptseite-schwesterprojekte .inhalt a { font-weight: bold; } /* p.catlinks span a[href*="/wiki/Kategorie:Arbeitskategorie"] { display:none } wegen HIDDENCAT nicht mehr notwendig */ /* Remove underline from IPA links */ .IPA a:link, .IPA a:visited { text-decoration: none; } span.Unicode { font-family: 'Code2000', 'Sun-ExtA', 'Arial Unicode MS', 'NSimSun', sans-serif; } span.Unicode1 { font-family: 'Code2001', 'Quivira', 'MPH 2B Damase', sans-serif; } span.Unicode2 { font-family: 'Sun-ExtB', 'Code2002', sans-serif; } span.IPA { font-family: 'Quivira', 'Code2000', 'Sun-ExtA', 'DejaVu Sans', 'Gentium', 'Arial Unicode MS', 'Lucida Sans Unicode', sans-serif; } span.IAST { font-family: 'Code2000', 'SunExtA', 'Arial Unicode MS', sans-serif; } span.altitalisch { font-family: 'Quivira', 'Code2001', 'MPH 2B Damase', sans-serif; } span.gotisch { font-family: 'Quivira', 'Code2001', 'MPH 2B Damase', sans-serif; } span.hebrew { font-family: 'Quivira', 'Sun-ExtA', 'Arial Unicode MS', 'SBL Hebrew', 'Code2000', 'MPH 2B Damase', sans-serif; } span.spanAr { font-family: 'Arial Unicode MS', 'Code2000', 'MPH 2B Damase', 'DejaVu Sans', sans-serif; } span.music-symbol { font-family: 'Musical Symbols', 'Euterpe', 'Code2001', sans-serif; } /* Standardmäßige Ausblendung der Flagged-Revisions-Backlog-Sitenotice */ #mw-oldreviewed-notice { display: none; } 8b220a7c628b982f0926ca85df2f1c635de8ebc9 2 9 26 2008-06-29T20:54:13Z Oliver 2 minimum info about myself wikitext text/x-wiki '''Oliver Beckstein''' is a sysadmin for the ''Biowerkzeug Community'' website. If you have questions or concerns you can [[Special:Emailuser/Oliver|email me]]. I am currently working at the [http://sbcb.bioch.ox.ac.uk/ Structural Bioinformatic and Computational Biochemistry Unit] at the University of Oxford where you can also [http://sbcb.bioch.ox.ac.uk/oliver/home.html find out more about myself]. &mdash; [[User:Oliver|Oli]] 20:54, 29 June 2008 (UTC) b59cf2ce864691b3ab78d9c8d6c3e1e23719ca7c 4 10 30 2008-06-29T21:29:59Z Oliver 2 link to com site wikitext text/x-wiki If you are a company and you want to purchase a license for [[Hippo]] then please proceed to [http://www.biowerkzeug.de/ biowerkzeug.de]. The ''biowerkzeug community'' is free and considers your contribution to it the most valuable payment. Thank you for visiting. 540f66f7e346e1499975fc13f2f90650576b3101 12 11 31 2008-06-29T21:43:45Z Oliver 2 basic instructions wikitext text/x-wiki == The ''biowerkzeug'' community == The ''biowerkzeug'' community site consists of the '''[http://wiki.biowerkzeug.org biowerkzeug Wiki]''' at [http://wiki.biowerkzeug.org/ wiki.biowerkzeug.org] (which you are reading right now) and the '''[http://forum.biowerkzeug.org/ biowerkzeug Forum]''' at [http://forum.biowerkzeug.org/ forum.biowerkzeug.org]. They were created as a place for users of the [[Hippo]] software and other biomolecular software packages to share ideas and help each other. Furthermore, developers frequent the sites as well and can add their insights and learn what the community wants to see implemented or fixed. == The Wiki == Anyone can read, search and browse the Wiki. Anyone who [[Special:Userlogin|registered]] and verified themselves with a valid email address may edit pages. See [[Help:Editing|Editing help]] to learn how to do this. If you have used [http://www.mediawiki.org MediaWiki] before then you may still want to have a look at the [[Help:Editing|Editing help]] page to see which additional extensions are enabled on this wiki. [[Category:Help]] 0d2063eb5dda35382cd96cb85d3ee43d445f4cdd 45 31 2008-06-29T22:47:13Z Oliver 2 /* The Wiki */ prefs wikitext text/x-wiki == The ''biowerkzeug'' community == The ''biowerkzeug'' community site consists of the '''[http://wiki.biowerkzeug.org biowerkzeug Wiki]''' at [http://wiki.biowerkzeug.org/ wiki.biowerkzeug.org] (which you are reading right now) and the '''[http://forum.biowerkzeug.org/ biowerkzeug Forum]''' at [http://forum.biowerkzeug.org/ forum.biowerkzeug.org]. They were created as a place for users of the [[Hippo]] software and other biomolecular software packages to share ideas and help each other. Furthermore, developers frequent the sites as well and can add their insights and learn what the community wants to see implemented or fixed. == The Wiki == Anyone can read, search and browse the Wiki. Anyone who [[Special:Userlogin|registered]] and verified themselves with a valid email address may edit pages. See [[Help:Editing|Editing help]] to learn how to do this. If you have used [http://www.mediawiki.org MediaWiki] before then you may still want to have a look at the [[Help:Editing|Editing help]] page to see which additional extensions are enabled on this wiki. As a registered user you can also set up your own "home page" (click on your name to edit it) or change your [[Special:Preferences|Preferences]]. For instance, you can allow other members to send you emails through the wiki or you can customize the way the wiki works. [[Category:Help]] c4e61725fa6dcab0ac3d03c1879300ecfc1d9d79 13 12 32 2008-06-29T21:44:44Z Oliver 2 special extensions page? wikitext text/x-wiki == Extensions == Is there a special wiki page that lists all installed [http://www.mediawiki.org/wiki/Category:Extensions|extensions]? &mdash; [[User:Oliver|Oli]] 21:44, 29 June 2008 (UTC) d3571660d6e5e93fc32e1b95150032c0b7e921d3 33 32 2008-06-29T21:45:10Z Oliver 2 /* Extensions */ wikitext text/x-wiki == Extensions == Is there a special wiki page that lists all installed [http://www.mediawiki.or/wiki/Category:Extensions extensions]? &mdash; [[User:Oliver|Oli]] 21:44, 29 June 2008 (UTC) 5cf766abd3b91abc626bf6fca9016cb7e61a8835 14 13 35 2008-06-29T21:51:35Z Oliver 2 New page: This category contains pages that tell you how to work with this Wiki; for instance, how to format entries in Wiki syntax, how to add images, but you can also learn more about the ''biower... wikitext text/x-wiki This category contains pages that tell you how to work with this Wiki; for instance, how to format entries in Wiki syntax, how to add images, but you can also learn more about the ''biowerkzeug'' community. 08ee63b0eecf398dda634b9d4d98d7e8e90a8c54 4 14 36 2008-06-29T22:01:50Z Oliver 2 basic privacy policy wikitext text/x-wiki The ''biowerkzeug'' community websites (the Forum and the Wiki) are managed by [http://www.biowerkzeug.com/ Biowerkzeug, Ltd]. We ask you to register with a valid email address in order to post to the Forum or edit the Wiki. This is done in the hope to have a minimum level of accountability and also to be able to recognize outstanding contributors. '''We will never use these email addresses or any other personal user information for marketing purposes or give or sell them to third parties.''' We have some precautionary measures in place to counteract spam but if they fail then please let us know, for instance by contacting [[User:Oliver|Oli]]. Also note that by default no-one can send email to you through the wiki. You will have to explicitly enable this feature in your [[Special:Preferences|Preferences]]. 829516717761a3d4536f8c20b914e21e06be8ed2 37 36 2008-06-29T22:04:18Z Oliver 2 Protected "[[Biowerkzeug Wiki:Privacy policy]]": protect page so that only sysops can edite them: Not everyone should be able to state company policy. [edit=sysop:move=sysop] [cascading] wikitext text/x-wiki The ''biowerkzeug'' community websites (the Forum and the Wiki) are managed by [http://www.biowerkzeug.com/ Biowerkzeug, Ltd]. We ask you to register with a valid email address in order to post to the Forum or edit the Wiki. This is done in the hope to have a minimum level of accountability and also to be able to recognize outstanding contributors. '''We will never use these email addresses or any other personal user information for marketing purposes or give or sell them to third parties.''' We have some precautionary measures in place to counteract spam but if they fail then please let us know, for instance by contacting [[User:Oliver|Oli]]. Also note that by default no-one can send email to you through the wiki. You will have to explicitly enable this feature in your [[Special:Preferences|Preferences]]. 829516717761a3d4536f8c20b914e21e06be8ed2 38 37 2008-06-29T22:04:57Z Oliver 2 help cat wikitext text/x-wiki The ''biowerkzeug'' community websites (the Forum and the Wiki) are managed by [http://www.biowerkzeug.com/ Biowerkzeug, Ltd]. We ask you to register with a valid email address in order to post to the Forum or edit the Wiki. This is done in the hope to have a minimum level of accountability and also to be able to recognize outstanding contributors. '''We will never use these email addresses or any other personal user information for marketing purposes or give or sell them to third parties.''' We have some precautionary measures in place to counteract spam but if they fail then please let us know, for instance by contacting [[User:Oliver|Oli]]. Also note that by default no-one can send email to you through the wiki. You will have to explicitly enable this feature in your [[Special:Preferences|Preferences]]. [[Category:Help]] 41b1030d1331f4ff6fa84f3fe726fbaa6447ff4f 4 15 39 2008-06-29T22:07:38Z Oliver 2 basic info wikitext text/x-wiki The ''biowerkzeug'' community site consists of the '''[http://wiki.biowerkzeug.org biowerkzeug Wiki]''' at [http://wiki.biowerkzeug.org/ wiki.biowerkzeug.org] (which you are reading right now) and the '''[http://forum.biowerkzeug.org/ biowerkzeug Forum]''' at [http://forum.biowerkzeug.org/ forum.biowerkzeug.org]. They were created as a place for users of the [[Hippo]] software and other biomolecular software packages to share ideas and help each other. Furthermore, developers frequent the sites as well and can add their insights and learn what the community wants to see implemented or fixed. The ''biowerkzeug'' community websites (the Forum and the Wiki) are managed by [http://www.biowerkzeug.com/ Biowerkzeug, Ltd]. [[Category:Help]] 85f72547b528b4a439a4dafc459ed57aaa7885af 46 39 2008-06-29T22:49:19Z Oliver 2 name wikitext text/x-wiki == The ''biowerkzeug'' community sites == The ''biowerkzeug'' community site consists of the '''[http://wiki.biowerkzeug.org biowerkzeug Wiki]''' at [http://wiki.biowerkzeug.org/ wiki.biowerkzeug.org] (which you are reading right now) and the '''[http://forum.biowerkzeug.org/ biowerkzeug Forum]''' at [http://forum.biowerkzeug.org/ forum.biowerkzeug.org]. They were created as a place for users of the [[Hippo]] software and other biomolecular software packages to share ideas and help each other. Furthermore, developers frequent the sites as well and can add their insights and learn what the community wants to see implemented or fixed. The ''biowerkzeug'' community websites (the Forum and the Wiki) are managed by [http://www.biowerkzeug.com/ Biowerkzeug, Ltd]. == The name == ''biowerkzeug'' is German and translates to ''bio-tool''. [[Category:Help]] 87dd7fe8b571687f44c3c2e8973dcf6698422d0d 47 46 2008-06-29T22:50:25Z Oliver 2 /* The biowerkzeug community sites */ wikitext text/x-wiki == The ''biowerkzeug'' community sites == The ''biowerkzeug'' community site consists of the '''[http://wiki.biowerkzeug.org biowerkzeug Wiki]''' at [http://wiki.biowerkzeug.org/ wiki.biowerkzeug.org] (which you are reading right now) and the '''[http://forum.biowerkzeug.org/ biowerkzeug Forum]''' at [http://forum.biowerkzeug.org/ forum.biowerkzeug.org]. They were created as a place for users of the [[Hippo]] software and other biomolecular software packages to share ideas and help each other. Furthermore, developers frequent the sites as well and can add their insights and learn what the community wants to see implemented or fixed. The ''biowerkzeug'' community websites (the Forum and the Wiki) are managed by [http://www.biowerkzeug.com/about.php Biowerkzeug, Ltd]. == The name == ''biowerkzeug'' is German and translates to ''bio-tool''. [[Category:Help]] f38bc0659515d2e5b8c8a561be576f0e043e0d24 4 16 40 2008-06-29T22:24:53Z Oliver 2 basic disclaimer wikitext text/x-wiki __NOTOC__ <div style="text-align: center; font-size: x-large; padding: 1em;">Biowerkzeug, Ltd. MAKES NO GUARANTEE OF VALIDITY</div> The ''biowerkzeug'' community sites (the [http://wiki.biowerkzeug.org/ Wiki] and the [http://forum.biowerkzeug.org/ Forum]) are created by the user community of [[Hippo]] and other biomolecular software. The opinions expressed here are the private opinions of the authors and not of ''Biowerkzeug, Ltd''. Please be aware that ''anyone'' with a valid account on the sites may edit the articles and no guarantee can be given for their correctness, fitness for any purpose (either explicitly expressed or implied), or legality in your jurisdiction. 7e640e94587bf0b6109865c0546bf71cfda441eb 41 40 2008-06-29T22:25:27Z Oliver 2 Protected "[[Biowerkzeug Wiki:General disclaimer]]": only Biowerkzeug Ltd should be able to change this [edit=sysop:move=sysop] wikitext text/x-wiki __NOTOC__ <div style="text-align: center; font-size: x-large; padding: 1em;">Biowerkzeug, Ltd. MAKES NO GUARANTEE OF VALIDITY</div> The ''biowerkzeug'' community sites (the [http://wiki.biowerkzeug.org/ Wiki] and the [http://forum.biowerkzeug.org/ Forum]) are created by the user community of [[Hippo]] and other biomolecular software. The opinions expressed here are the private opinions of the authors and not of ''Biowerkzeug, Ltd''. Please be aware that ''anyone'' with a valid account on the sites may edit the articles and no guarantee can be given for their correctness, fitness for any purpose (either explicitly expressed or implied), or legality in your jurisdiction. 7e640e94587bf0b6109865c0546bf71cfda441eb 42 41 2008-06-29T22:26:04Z Oliver 2 wikitext text/x-wiki __NOTOC__ <div style="text-align: center; font-size: x-large; padding: 1em;">Biowerkzeug, Ltd. MAKES NO GUARANTEE OF VALIDITY</div> The ''biowerkzeug'' community sites (the [http://wiki.biowerkzeug.org/ Wiki] and the [http://forum.biowerkzeug.org/ Forum]) are created by the user community of [[Hippo]] and other biomolecular software. The opinions expressed here are the private opinions of the authors and not of ''Biowerkzeug, Ltd''. Please be aware that ''anyone'' with a valid account on the sites may edit the articles and no guarantee can be given for their correctness, fitness for any purpose (either explicitly expressed or implied), or legality in your jurisdiction. [[Category:Help]] 583ccdedd2ccfcf96cda210bbd07853230934090 4 17 43 2008-06-29T22:36:21Z Oliver 2 links wikitext text/x-wiki The ''biowerkzeug'' community consists of: ;[http://forum.biowerkzeug.org Forum]: The Forum is a Bulletin Board in which users can ask questions and other users and developers can enter dicussions. The format is very informal. ;[http://wiki.biowerkzeug.org Wiki]: The Wiki contains How-to documents, background material, and links to other interesting material. Interesting threads from the Forum are copied to the Wiki and reformatted as new articles. The ''biowerkzeug'' community sites are run by ''[http://www.biowerkzeug.com/about.php Biowerkzeug, Ltd]''. The [http://www.biowerkzeug.com/ biowerkzeug.com] site contains information about the commercially licensed version of the [[Hippo]] software. [[Category:Help]] 91805fb5e093f3388c005a9b997d08c4f485d3e8 44 43 2008-06-29T22:36:46Z Oliver 2 wikitext text/x-wiki The ''biowerkzeug'' community consists of: ;[http://forum.biowerkzeug.org Forum]: The Forum is a Bulletin Board in which users can ask questions and other users and developers can enter dicussions. The format is very informal. ;[http://wiki.biowerkzeug.org Wiki]: The Wiki contains How-to documents, background material, and links to other interesting material. Interesting threads from the Forum are copied to the Wiki and reformatted as new articles. The ''biowerkzeug'' community sites are run by ''[http://www.biowerkzeug.com/about.php Biowerkzeug, Ltd]''. The '''[http://www.biowerkzeug.com/ biowerkzeug.com]''' site contains information about the commercially licensed version of the [[Hippo]] software. [[Category:Help]] 0ef27ae62a089c7fc1751405d65d460134bea87c 0 18 49 2008-06-30T15:00:09Z Oliver 2 new; copied from Woolf wiki wikitext text/x-wiki This page collects software that we find useful to display data from running molecular simulations. A special section is dedicated to [[#Rendering|Render]] software that create photorealistic or artistic images from scenes exported from other visualization software. == Molecules in 3D == * [[VMD]]; also has extensive analysis and model build capabilities * [[pyMol]] * [[chimera]] * [[yasara]] * [[QuteMol]] * [[pyQuteMol]] == 1D and 2D data == * [[xfarbe]], a simple 2D plotter * [[xmgrace]], for 1D plots and some graph analysis * gnuplot * [[matplotlib]], a python based scientific plotting library * [[R]] == 3D data == To display 3D data such as densities, you can use a typically insanely powerful 3D visualization package; see for instance this list of [http://prism.dkrz.de/Workpackages/WP4a/Low-End/Packages/WP4a_Low-End_graphic_packages.html graphics packages]. * [http://www.opendx.org/ OpenDX]: list of [http://www.opendx.org/support.html documentation] and [http://opendx.sdsc.edu/docs/html/pages/usrgu068.htm#HDREDF native DX file format] * viewers based on [http://www.vtk.org/ VTK] such as [http://mayavi.sourceforge.net/ MayaVi] * [[VMD]] and [[Chimera]] == Rendering == * [[Raster3D]] (the renderer can be called from [[VMD]]) and VMD's [[VMD#Tachyon|Tachyon]]. * [[Gelato]] * [[Pixie]], a Renderman-compatible shader [[Category:Visualization]] [[Category:Software]] cce8ceb4b699687fb955388dd8b8bd63e68f3e4d 14 19 50 2008-06-30T15:01:22Z Oliver 2 New page: This category contains pages that deal with software packages. Expect to find short introductions, helpful hints, and links how to obtain the software. wikitext text/x-wiki This category contains pages that deal with software packages. Expect to find short introductions, helpful hints, and links how to obtain the software. 9551304a191143ada632763b4290df500b8c0293 14 20 51 2008-06-30T15:02:32Z Oliver 2 New page: The '''Visualization''' category contains articles on how to create images of molecular simulations and also how to display other data derived from simulations. wikitext text/x-wiki The '''Visualization''' category contains articles on how to create images of molecular simulations and also how to display other data derived from simulations. 80f32277f6a693f0a42036fa583715142b409571 0 1 52 48 2008-06-30T15:03:21Z Oliver 2 /* Visualization */ more succinct wikitext text/x-wiki <div id="hauptseite"> {| width="100%" cellspacing="0" cellpadding="0" | colspan="2" | This Wiki discusses biomolecular simulations with [[Hippo]] and other molecular dynamics/Monte Carlo codes. It serves as a repository for the community and complements the [http://forums.biowerkzeug.org forums]. Please contribute your own knowledge to this Wiki: If anything is unclear and you know how to write it better – change it. If you have useful tips & tricks – share them with everyone else. If you have comments on any article in this Wiki – start a discussion on the ''discussion'' page that accompanies every article (look in the top menu bar). We only ask you to [[Special:Userlogin|register]] when you edit pages. See [[Help:Editing|Help&rarr;Editing]] to get started on contributing to this community resource. |- | width="50%" style="vertical-align:top;" | <div id="Hippo" class="hauptseite-links"> == Hippo == <div class="inhalt"> * [[Simulations]] * [[Analysis]] * [[Graphical interface]] * [[Files and features]] </div> </div> <div id="Methods" class="hauptseite-links"> == Methods == <div class="inhalt"> * [[Molecular dynamics]] * [[Monte Carlo]] * [[Force fields]] * [[Algorithms]] * [[Solvents]] * [[Membranes]] </div> </div> | width="50%" style="vertical-align:top;" | <div id="Simulation protocols" class="hauptseite-rechts"> == Simulation protocols == <div class="inhalt"> * [[Globular proteins]] in solvent * [[Membrane proteins]] in membrane and solvent * [[Free energy calculations]] * [[Transition path sampling]] </div> </div> <div id="Visualization" class="hauptseite-rechts"> == Visualization == <div class="inhalt"> * [[Visualization software|Software]] * [[Visualization tutorial|tutorial]] with [[VMD]] * [[Movie tutorial]] </div> </div> <div id="Software" class="hauptseite-rechts"> == Software == <div class="inhalt"> * [[Molecular dynamics codes]] * [[Monte Carlo codes]] * [[Electrostatics]] and [[Brownian dynamics]] * [[Model building]] * [[Visualization software|Visualization]] * [[Analysis software]] </div> </div> |} </div> __NOTOC__ e60b68dd797aaf8688dc94aadb36437f2d6267a4 68 52 2008-06-30T15:54:07Z Oliver 2 browse by category wikitext text/x-wiki <div id="hauptseite"> {| width="100%" cellspacing="0" cellpadding="0" | colspan="2" | This Wiki discusses biomolecular simulations with [[Hippo]] and other molecular dynamics/Monte Carlo codes. It serves as a repository for the community and complements the [http://forums.biowerkzeug.org forums]. Please contribute your own knowledge to this Wiki: If anything is unclear and you know how to write it better – change it. If you have useful tips & tricks – share them with everyone else. If you have comments on any article in this Wiki – start a discussion on the ''discussion'' page that accompanies every article (look in the top menu bar). We only ask you to [[Special:Userlogin|register]] when you edit pages. See [[Help:Editing|Help&rarr;Editing]] to get started on contributing to this community resource. Follow the links below, use the search on the left, or browse articles by [[Special:Categories|category]]. |- | width="50%" style="vertical-align:top;" | <div id="Hippo" class="hauptseite-links"> == Hippo == <div class="inhalt"> * [[Simulations]] * [[Analysis]] * [[Graphical interface]] * [[Files and features]] </div> </div> <div id="Methods" class="hauptseite-links"> == Methods == <div class="inhalt"> * [[Molecular dynamics]] * [[Monte Carlo]] * [[Force fields]] * [[Algorithms]] * [[Solvents]] * [[Membranes]] </div> </div> | width="50%" style="vertical-align:top;" | <div id="Simulation protocols" class="hauptseite-rechts"> == Simulation protocols == <div class="inhalt"> * [[Globular proteins]] in solvent * [[Membrane proteins]] in membrane and solvent * [[Free energy calculations]] * [[Transition path sampling]] </div> </div> <div id="Visualization" class="hauptseite-rechts"> == Visualization == <div class="inhalt"> * [[Visualization software|Software]] * [[Visualization tutorial|tutorial]] with [[VMD]] * [[Movie tutorial]] </div> </div> <div id="Software" class="hauptseite-rechts"> == Software == <div class="inhalt"> * [[Molecular dynamics codes]] * [[Monte Carlo codes]] * [[Electrostatics]] and [[Brownian dynamics]] * [[Model building]] * [[Visualization software|Visualization]] * [[Analysis software]] </div> </div> |} </div> __NOTOC__ 451f3541cceab2b2eae7eb8d62ee2ddb968ada9d 97 68 2008-10-02T21:05:56Z Oliver 2 bold faced Hippo wikitext text/x-wiki <div id="hauptseite"> {| width="100%" cellspacing="0" cellpadding="0" | colspan="2" | This Wiki discusses biomolecular simulations with '''[[Hippo]]''' and other molecular dynamics/Monte Carlo codes. It serves as a repository for the community and complements the [http://forums.biowerkzeug.org forums]. Please contribute your own knowledge to this Wiki: If anything is unclear and you know how to write it better – change it. If you have useful tips & tricks – share them with everyone else. If you have comments on any article in this Wiki – start a discussion on the ''discussion'' page that accompanies every article (look in the top menu bar). We only ask you to [[Special:Userlogin|register]] when you edit pages. See [[Help:Editing|Help&rarr;Editing]] to get started on contributing to this community resource. Follow the links below, use the search on the left, or browse articles by [[Special:Categories|category]]. |- | width="50%" style="vertical-align:top;" | <div id="Hippo" class="hauptseite-links"> == Hippo == <div class="inhalt"> * [[Simulations]] * [[Analysis]] * [[Graphical interface]] * [[Files and features]] </div> </div> <div id="Methods" class="hauptseite-links"> == Methods == <div class="inhalt"> * [[Molecular dynamics]] * [[Monte Carlo]] * [[Force fields]] * [[Algorithms]] * [[Solvents]] * [[Membranes]] </div> </div> | width="50%" style="vertical-align:top;" | <div id="Simulation protocols" class="hauptseite-rechts"> == Simulation protocols == <div class="inhalt"> * [[Globular proteins]] in solvent * [[Membrane proteins]] in membrane and solvent * [[Free energy calculations]] * [[Transition path sampling]] </div> </div> <div id="Visualization" class="hauptseite-rechts"> == Visualization == <div class="inhalt"> * [[Visualization software|Software]] * [[Visualization tutorial|tutorial]] with [[VMD]] * [[Movie tutorial]] </div> </div> <div id="Software" class="hauptseite-rechts"> == Software == <div class="inhalt"> * [[Molecular dynamics codes]] * [[Monte Carlo codes]] * [[Electrostatics]] and [[Brownian dynamics]] * [[Model building]] * [[Visualization software|Visualization]] * [[Analysis software]] </div> </div> |} </div> __NOTOC__ d323232ec652f07d9ac4338efde3bfdbf04ac46d 98 97 2008-10-02T21:06:56Z Oliver 2 /* Hippo */ Features wikitext text/x-wiki <div id="hauptseite"> {| width="100%" cellspacing="0" cellpadding="0" | colspan="2" | This Wiki discusses biomolecular simulations with '''[[Hippo]]''' and other molecular dynamics/Monte Carlo codes. It serves as a repository for the community and complements the [http://forums.biowerkzeug.org forums]. Please contribute your own knowledge to this Wiki: If anything is unclear and you know how to write it better – change it. If you have useful tips & tricks – share them with everyone else. If you have comments on any article in this Wiki – start a discussion on the ''discussion'' page that accompanies every article (look in the top menu bar). We only ask you to [[Special:Userlogin|register]] when you edit pages. See [[Help:Editing|Help&rarr;Editing]] to get started on contributing to this community resource. Follow the links below, use the search on the left, or browse articles by [[Special:Categories|category]]. |- | width="50%" style="vertical-align:top;" | <div id="Hippo" class="hauptseite-links"> == Hippo == <div class="inhalt"> * [[Hippo|Features]] * [[Simulations]] * [[Analysis]] * [[Graphical interface]] * [[Files]] </div> </div> <div id="Methods" class="hauptseite-links"> == Methods == <div class="inhalt"> * [[Molecular dynamics]] * [[Monte Carlo]] * [[Force fields]] * [[Algorithms]] * [[Solvents]] * [[Membranes]] </div> </div> | width="50%" style="vertical-align:top;" | <div id="Simulation protocols" class="hauptseite-rechts"> == Simulation protocols == <div class="inhalt"> * [[Globular proteins]] in solvent * [[Membrane proteins]] in membrane and solvent * [[Free energy calculations]] * [[Transition path sampling]] </div> </div> <div id="Visualization" class="hauptseite-rechts"> == Visualization == <div class="inhalt"> * [[Visualization software|Software]] * [[Visualization tutorial|tutorial]] with [[VMD]] * [[Movie tutorial]] </div> </div> <div id="Software" class="hauptseite-rechts"> == Software == <div class="inhalt"> * [[Molecular dynamics codes]] * [[Monte Carlo codes]] * [[Electrostatics]] and [[Brownian dynamics]] * [[Model building]] * [[Visualization software|Visualization]] * [[Analysis software]] </div> </div> |} </div> __NOTOC__ e3565c13e6dd618ed3e7cf49b76a87b3adce381a 0 21 53 2008-06-30T15:10:51Z Oliver 2 basic list wikitext text/x-wiki A non-exhaustive list of codes available to the academic community to perform [[Molecular dynamics simulations]] of biological molecules. For all codes listed the source code is available. == Free for academics == * [[Hippo]] * [[Gromacs]] * [[LAMMPS]] * [[NAMD]] * [[DL_POLY]] == Nominal fee for academics == * [[Charmm]] * [[Amber]] cc7ae9b5d13309b704b614587342e83e85d22415 57 53 2008-06-30T15:20:58Z Oliver 2 wikitext text/x-wiki A non-exhaustive list of codes available to the academic community to perform [[Molecular dynamics simulations]] of biological molecules. For all codes listed the source code is available. == Free for academics == * [[Hippo]] * [[Gromacs]] * [[LAMMPS]] * [[NAMD]] * [[DL_POLY]] == Nominal fee for academics == * [[Charmm]] * [[Amber]] [[Category:Molecular Dynamics]] [[Category:Software]] 850942a125b0dfe28cbee1e51a1d457944cea23e 0 22 54 2008-06-30T15:12:39Z Oliver 2 basic list wikitext text/x-wiki A non-exhaustive list of codes available to the academic community to perform [[Monte Carlo simulations]] of biomolecules. For all codes listed, source code is available. == Free for academics == * [[Hippo]] == Nominal fee for academics == * [[Charmm]] 4c068bf6a9d96e90fa7c46fdebe82c93f9687e55 60 54 2008-06-30T15:23:37Z Oliver 2 wikitext text/x-wiki A non-exhaustive list of codes available to the academic community to perform [[Monte Carlo simulations]] of biomolecules. For all codes listed, source code is available. == Free for academics == * [[Hippo]] == Nominal fee for academics == * [[Charmm]] [[Category:Monte Carlo]] [[Category:Software]] 2456e2389800866fee1c69a51dd16a344fe4fbf3 94 60 2008-07-07T18:03:25Z Martin 5 wikitext text/x-wiki A non-exhaustive list of codes available to the academic community to perform [[Monte Carlo simulations]] of biomolecules. For all codes listed, source code is available. == Free for academics == * [[Hippo]] == Nominal fee for academics == * [[Charmm]] * [[BOSS]] [[Category:Monte Carlo]] [[Category:Software]] 1bf08e65311907eec8ccf939fa43b146b7d639c9 0 23 55 2008-06-30T15:18:17Z Oliver 2 basic list wikitext text/x-wiki A non-exhaustive list of codes available to the academic community to perform calculations of electrostatic fields, typically solving the [[Poisson-Boltzmann equation]] or approximating it using the [[Generalized Born method]]. == Free for academic users == * [[APBS]] * [[Hippo]] * [[VMD]] together with [[APBS]] or PME electrostatics == Nominal fee == * [[DelPhi]] * [[UHBD]] (can also do Brownian Dynamics) * [[Charmm]] (PBEQ module, can also use [[APBS]]) [[Category:Electrostatics]] [[Category:Software]] 3b1e0a2068b7cb02e1d3eae6c4b4e9f595c3bdc4 14 24 56 2008-06-30T15:20:14Z Oliver 2 New page: Articles in this category deal with the question of how to calculate and represent the electrostatic field around a molecule that is due to the protein, the inhomogeneous ion distribution ... wikitext text/x-wiki Articles in this category deal with the question of how to calculate and represent the electrostatic field around a molecule that is due to the protein, the inhomogeneous ion distribution around it, and external potentials. 3318aed6d979bc453e3052a47952762cd4a141c1 14 25 58 2008-06-30T15:22:51Z Oliver 2 New page: The articles below are concerned with '''[[Molecular Dynamics]]''' ('''MD'''), a method that simulates a system of many interacting particles by calculating the forces on all atoms at each... wikitext text/x-wiki The articles below are concerned with '''[[Molecular Dynamics]]''' ('''MD'''), a method that simulates a system of many interacting particles by calculating the forces on all atoms at each time step and propagating the coordinates of these particles through time via [[Newton's equations of motion]]. 36a8efe23d77235c44c1576c4b656d87af15137f 59 58 2008-06-30T15:23:04Z Oliver 2 wikitext text/x-wiki The articles below are concerned with '''[[Molecular Dynamics]]''' ('''MD'''), a method that simulates a system of many interacting particles by calculating the forces on all atoms at each time step and propagating the coordinates of these particles through time via [[Newton's equations of motions]]. bd257df0fa9c2b4b2496dae920fded2592e634dc 14 26 61 2008-06-30T15:25:46Z Oliver 2 New page: Articles below describe and discuss the '''[[Monte Carlo]]''' ('''MC''') method. Using MC one can sample configurations of a system of many interacting particles according to their (equili... wikitext text/x-wiki Articles below describe and discuss the '''[[Monte Carlo]]''' ('''MC''') method. Using MC one can sample configurations of a system of many interacting particles according to their (equilibrium) Boltzmann weight. Hence averages of observables over those configurations are true equilibrium averages. 53d627a929d51eb5ea40f1912f79701c78ae4e35 0 27 62 2008-06-30T15:26:52Z Oliver 2 stub wikitext text/x-wiki ;[[Modeller]]: does homology building. ;[[Dowser]]: can help you to solvate a protein before simulations. ;[[VMD]]: comes with a lot of useful modeling tools in ''Extensions'' &rarr; ''Modeling''; it can auto-build xplor-style psf files, add ions to the system, solvate, mutate, ... ;[[Charmm]]: has a fairly complete (but as always, idiosyncratic) model building facility with the IC commands. [[Category:Modelling]] [[Category:Software]] 1219ae0c793d56918905b860705dc55ecd38692b 14 28 63 2008-06-30T15:28:50Z Oliver 2 New page: Articles in this category deal with the question how to create, fix, or improve structures, setup membrane systems, solvate a protein, and generally help you to obtain a starting configura... wikitext text/x-wiki Articles in this category deal with the question how to create, fix, or improve structures, setup membrane systems, solvate a protein, and generally help you to obtain a starting configuration for a [[Molecular dynamics simulations|MD]] or [[Monte Carlo simulations|MC]] simulation. 60d03d17cd76f9013b958e99ffa512413db578c8 0 29 64 2008-06-30T15:47:39Z Oliver 2 basic analysis list (Woolf Wiki + changes) wikitext text/x-wiki Running simulations is often the easy bit. The hard bit is to extract meaningful information from the Gigabytes of trajectory data. This list can act as a starting point. For most advanced uses, however, one will probably have to write analysis code in [[python]], [[Perl]], [[tcl]], [[C/C++]], [[bash]] ... or any other language that "gets the job done". == "Native" tools == Many of the [[Molecular dynamics software|MD packages]] come with their own analysis tools or scripting language. Sometimes it is possible to [[convert data formats]] between packages and use the other package's analysis tools. ;[[Gromacs]] analysis tools: oone of the strengths of Gromacs is that it comes with a large number of useful analysis tools that make many of the standard analysis tasks simple to perform ;NAMD/[[VMD]]: VMD can be used through its GUI or by scripting it in [[tcl]] to great effect ;[[Charmm]]: Charmm is feature-rich but its scripting language can cause a steep learning curve ;LAMMPS/[[pizza]]: pizza.py is a python library geared towards output from [[LAMMPS]] == MD Analysis libraries == ;[[MDAnalysis]]: a python library to analyze dcd trajectories (in conjunction with a psf) ;Amber/[[ptraj]]: command-line based analysis ;[http://dirac.cnrs-orleans.fr/MMTK/ MMTK]: Another python-based framework for doing analysis is the ''Molecular Modelling Tool Kit''. However, it does not natively read [[Charmm]] dcd files and hence it can be cumbersome to use. == Specialized tools == ;[[HOLE]]: Oliver Smart's program to trace out pore surfaces and estimate single channel conductances. ;CAVER: [http://loschmidt.chemi.muni.cz/caver/index.php CAVER] provides rapid, accurate and fully automated calculation of pathways leading from buried cavities to outside solvent in static and dynamic protein structures. Calculated pathways can be visualized by graphic program PyMol dissecting anatomy and dynamics of entrance tunnels. CAVER allows analysis of any molecular structure including proteins, nucleic acids, inorganic materials, etc. CAVER is available as [http://loschmidt.chemi.muni.cz/caver/online.php online version] or [[PyMol]] plugin suitable for calculation of pathways in discrete protein structures and stand alone version enabling analysis of trajectories from the molecular dynamics simulations. ;[http://swift.cmbi.ru.nl/gv/dssp/ dssp]: ''Definition of secondary structure of proteins given a set of 3D coordinates.'' The DSSP program defines secondary structure, geometrical features and solvent exposure of proteins, given atomic coordinates in Protein Data Bank format. The program does NOT PREDICT protein structure. According to the Science Citation Index (July 1995), the program has been cited in the scientific literature more than 1000 times. ; [http://www.compbio.dundee.ac.uk/manuals/stamp.4.2/stamp.html STAMP]: ''Structural Alignment of Multiple Proteins''. STAMP is a package for the alignment of protein sequence based on three-dimensional (3D) structure. It provides not only multiple alignments and the corresponding `best-fit' superimpositions, but also a systematic and reproducible method for assessing the quality of such alignments. It also provides a method for protein 3D structure data base scanning. In addition to structure comparison, the STAMP package provides input for programs to display and analyse protein sequence alignments and tertiary structures. Please note that, although STAMP outputs a sequence alignment, it is a program for 3D structures, and NOT sequences. ;[[swinker]]: finds and calculates helix hinges. It optionally finds the hinge point and calculates kink and swivel angles. == General purpose mathematical packages == ;[[Scientific Python]] and [[pylab]]: a [[matlab]]-like [[python]] module that has sophisticated analysis and plotting capabilities ;[[matlab]]: ;[[Mathematica]]: ;[[R]]: R is a language and environment for statistical computing and graphics. R provides a wide variety of statistical (linear and nonlinear modelling, classical statistical tests, time-series analysis, classification, clustering, ...) and graphical techniques, and is highly extensible. One of R's strengths is the ease with which well-designed publication-quality plots can be produced, including mathematical symbols and formulae where needed. Great care has been taken over the defaults for the minor design choices in graphics, but the user retains full control. 30f0beb5055e40b7daae3bf272c6f7fb06df203c 65 64 2008-06-30T15:48:23Z Oliver 2 wikitext text/x-wiki Running simulations is often the easy bit. The hard bit is to extract meaningful information from the Gigabytes of trajectory data. This list can act as a starting point. For most advanced uses, however, one will probably have to write analysis code in [[python]], [[Perl]], [[tcl]], [[C/C++]], [[bash]] ... or any other language that "gets the job done". == "Native" tools == Many of the [[Molecular dynamics software|MD packages]] come with their own analysis tools or scripting language. Sometimes it is possible to [[convert data formats]] between packages and use the other package's analysis tools. ;[[Gromacs]] analysis tools: oone of the strengths of Gromacs is that it comes with a large number of useful analysis tools that make many of the standard analysis tasks simple to perform ;NAMD/[[VMD]]: VMD can be used through its GUI or by scripting it in [[tcl]] to great effect ;[[Charmm]]: Charmm is feature-rich but its scripting language can cause a steep learning curve ;LAMMPS/[[pizza]]: pizza.py is a python library geared towards output from [[LAMMPS]] ;Amber/[[ptraj]]: command-line based analysis == MD Analysis libraries == ;[[MDAnalysis]]: a python library to analyze dcd trajectories (in conjunction with a psf) ;[http://dirac.cnrs-orleans.fr/MMTK/ MMTK]: Another python-based framework for doing analysis is the ''Molecular Modelling Tool Kit''. However, it does not natively read [[Charmm]] dcd files and hence it can be cumbersome to use. == Specialized tools == ;[[HOLE]]: Oliver Smart's program to trace out pore surfaces and estimate single channel conductances. ;CAVER: [http://loschmidt.chemi.muni.cz/caver/index.php CAVER] provides rapid, accurate and fully automated calculation of pathways leading from buried cavities to outside solvent in static and dynamic protein structures. Calculated pathways can be visualized by graphic program PyMol dissecting anatomy and dynamics of entrance tunnels. CAVER allows analysis of any molecular structure including proteins, nucleic acids, inorganic materials, etc. CAVER is available as [http://loschmidt.chemi.muni.cz/caver/online.php online version] or [[PyMol]] plugin suitable for calculation of pathways in discrete protein structures and stand alone version enabling analysis of trajectories from the molecular dynamics simulations. ;[http://swift.cmbi.ru.nl/gv/dssp/ dssp]: ''Definition of secondary structure of proteins given a set of 3D coordinates.'' The DSSP program defines secondary structure, geometrical features and solvent exposure of proteins, given atomic coordinates in Protein Data Bank format. The program does NOT PREDICT protein structure. According to the Science Citation Index (July 1995), the program has been cited in the scientific literature more than 1000 times. ; [http://www.compbio.dundee.ac.uk/manuals/stamp.4.2/stamp.html STAMP]: ''Structural Alignment of Multiple Proteins''. STAMP is a package for the alignment of protein sequence based on three-dimensional (3D) structure. It provides not only multiple alignments and the corresponding `best-fit' superimpositions, but also a systematic and reproducible method for assessing the quality of such alignments. It also provides a method for protein 3D structure data base scanning. In addition to structure comparison, the STAMP package provides input for programs to display and analyse protein sequence alignments and tertiary structures. Please note that, although STAMP outputs a sequence alignment, it is a program for 3D structures, and NOT sequences. ;[[swinker]]: finds and calculates helix hinges. It optionally finds the hinge point and calculates kink and swivel angles. == General purpose mathematical packages == ;[[Scientific Python]] and [[pylab]]: a [[matlab]]-like [[python]] module that has sophisticated analysis and plotting capabilities ;[[matlab]]: ;[[Mathematica]]: ;[[R]]: R is a language and environment for statistical computing and graphics. R provides a wide variety of statistical (linear and nonlinear modelling, classical statistical tests, time-series analysis, classification, clustering, ...) and graphical techniques, and is highly extensible. One of R's strengths is the ease with which well-designed publication-quality plots can be produced, including mathematical symbols and formulae where needed. Great care has been taken over the defaults for the minor design choices in graphics, but the user retains full control. 8b0ca8ae131b784871d1f4ccdb2bba52e4677e8e 66 65 2008-06-30T15:49:00Z Oliver 2 categories wikitext text/x-wiki Running simulations is often the easy bit. The hard bit is to extract meaningful information from the Gigabytes of trajectory data. This list can act as a starting point. For most advanced uses, however, one will probably have to write analysis code in [[python]], [[Perl]], [[tcl]], [[C/C++]], [[bash]] ... or any other language that "gets the job done". == "Native" tools == Many of the [[Molecular dynamics software|MD packages]] come with their own analysis tools or scripting language. Sometimes it is possible to [[convert data formats]] between packages and use the other package's analysis tools. ;[[Gromacs]] analysis tools: oone of the strengths of Gromacs is that it comes with a large number of useful analysis tools that make many of the standard analysis tasks simple to perform ;NAMD/[[VMD]]: VMD can be used through its GUI or by scripting it in [[tcl]] to great effect ;[[Charmm]]: Charmm is feature-rich but its scripting language can cause a steep learning curve ;LAMMPS/[[pizza]]: pizza.py is a python library geared towards output from [[LAMMPS]] ;Amber/[[ptraj]]: command-line based analysis == MD Analysis libraries == ;[[MDAnalysis]]: a python library to analyze dcd trajectories (in conjunction with a psf) ;[http://dirac.cnrs-orleans.fr/MMTK/ MMTK]: Another python-based framework for doing analysis is the ''Molecular Modelling Tool Kit''. However, it does not natively read [[Charmm]] dcd files and hence it can be cumbersome to use. == Specialized tools == ;[[HOLE]]: Oliver Smart's program to trace out pore surfaces and estimate single channel conductances. ;CAVER: [http://loschmidt.chemi.muni.cz/caver/index.php CAVER] provides rapid, accurate and fully automated calculation of pathways leading from buried cavities to outside solvent in static and dynamic protein structures. Calculated pathways can be visualized by graphic program PyMol dissecting anatomy and dynamics of entrance tunnels. CAVER allows analysis of any molecular structure including proteins, nucleic acids, inorganic materials, etc. CAVER is available as [http://loschmidt.chemi.muni.cz/caver/online.php online version] or [[PyMol]] plugin suitable for calculation of pathways in discrete protein structures and stand alone version enabling analysis of trajectories from the molecular dynamics simulations. ;[http://swift.cmbi.ru.nl/gv/dssp/ dssp]: ''Definition of secondary structure of proteins given a set of 3D coordinates.'' The DSSP program defines secondary structure, geometrical features and solvent exposure of proteins, given atomic coordinates in Protein Data Bank format. The program does NOT PREDICT protein structure. According to the Science Citation Index (July 1995), the program has been cited in the scientific literature more than 1000 times. ; [http://www.compbio.dundee.ac.uk/manuals/stamp.4.2/stamp.html STAMP]: ''Structural Alignment of Multiple Proteins''. STAMP is a package for the alignment of protein sequence based on three-dimensional (3D) structure. It provides not only multiple alignments and the corresponding `best-fit' superimpositions, but also a systematic and reproducible method for assessing the quality of such alignments. It also provides a method for protein 3D structure data base scanning. In addition to structure comparison, the STAMP package provides input for programs to display and analyse protein sequence alignments and tertiary structures. Please note that, although STAMP outputs a sequence alignment, it is a program for 3D structures, and NOT sequences. ;[[swinker]]: finds and calculates helix hinges. It optionally finds the hinge point and calculates kink and swivel angles. == General purpose mathematical packages == ;[[Scientific Python]] and [[pylab]]: a [[matlab]]-like [[python]] module that has sophisticated analysis and plotting capabilities ;[[matlab]]: ;[[Mathematica]]: ;[[R]]: R is a language and environment for statistical computing and graphics. R provides a wide variety of statistical (linear and nonlinear modelling, classical statistical tests, time-series analysis, classification, clustering, ...) and graphical techniques, and is highly extensible. One of R's strengths is the ease with which well-designed publication-quality plots can be produced, including mathematical symbols and formulae where needed. Great care has been taken over the defaults for the minor design choices in graphics, but the user retains full control. [[Category:Analysis]] [[Category:Software]] db22d157f9708c4319fe9758603372bb442735b9 14 30 67 2008-06-30T15:50:40Z Oliver 2 New page: Running simulations is often the easy bit. The hard bit is to extract meaningful information from the Gigabytes of trajectory data. Articles in this category give hints on what programs to... wikitext text/x-wiki Running simulations is often the easy bit. The hard bit is to extract meaningful information from the Gigabytes of trajectory data. Articles in this category give hints on what programs to use to perform analysis and how to do it. 5de288a22de7b949608b9b0cc9990a99cdd4dd27 0 3 69 9 2008-06-30T19:31:55Z Orbeckst 7 wikitext text/x-wiki Simulating the motion of molecules by iteratively solving [[Newton's equations of motion]]. = Integrators = * [[Verlet]] * [[Velocity Verlet]] d37f4a1677923cc45d4635d5eedc1de22f03a960 4 10 70 30 2008-06-30T19:33:54Z Orbeckst 7 main commercial site is .com wikitext text/x-wiki If you are a company and you want to purchase a license for [[Hippo]] then please proceed to [http://www.biowerkzeug.com/ biowerkzeug.com]. The ''biowerkzeug community'' is free and considers your contribution to it the most valuable payment. Thank you for visiting. 0114f8b31940b6c0fa144b4321a42a8d8bdc543d 0 18 71 49 2008-06-30T19:35:19Z Orbeckst 7 /* Molecules in 3D */ wikitext text/x-wiki This page collects software that we find useful to display data from running molecular simulations. A special section is dedicated to [[#Rendering|Render]] software that create photorealistic or artistic images from scenes exported from other visualization software. == Molecules in 3D == * [[VMD]]; also has extensive analysis and model building capabilities * [[pyMol]] * [[chimera]] * [[yasara]] * [[QuteMol]] * [[pyQuteMol]] == 1D and 2D data == * [[xfarbe]], a simple 2D plotter * [[xmgrace]], for 1D plots and some graph analysis * gnuplot * [[matplotlib]], a python based scientific plotting library * [[R]] == 3D data == To display 3D data such as densities, you can use a typically insanely powerful 3D visualization package; see for instance this list of [http://prism.dkrz.de/Workpackages/WP4a/Low-End/Packages/WP4a_Low-End_graphic_packages.html graphics packages]. * [http://www.opendx.org/ OpenDX]: list of [http://www.opendx.org/support.html documentation] and [http://opendx.sdsc.edu/docs/html/pages/usrgu068.htm#HDREDF native DX file format] * viewers based on [http://www.vtk.org/ VTK] such as [http://mayavi.sourceforge.net/ MayaVi] * [[VMD]] and [[Chimera]] == Rendering == * [[Raster3D]] (the renderer can be called from [[VMD]]) and VMD's [[VMD#Tachyon|Tachyon]]. * [[Gelato]] * [[Pixie]], a Renderman-compatible shader [[Category:Visualization]] [[Category:Software]] 43905c954d60efeb6ecd6eb7616dbe8c9f4354b7 0 31 72 2008-06-30T19:40:31Z Orbeckst 7 from Woolf Wiki (main author Juan R Perilla) wikitext text/x-wiki [http://www.r-project.org/ R] (also known as the '''R project''') is a free software environment and language for statistical computing and graphics. It compiles and runs on a wide variety of UNIX platforms, Windows and MacOS. ''R'' is a free implementation of the statistical programming language ''S'' and ''S-Plus'' developed at Bell labs on the 80-90s. It is object oriented and provides several tools for statistical analysis, however it can be used for data manipulation, calculation and graphical display as well. Notably, it can be used from [[python]] using '''[[rpy]]''' which makes all R functions available to python. == Documentation == Essential reading * [http://cran.r-project.org/doc/manuals/R-intro.html An introduction to R] * [http://cran.r-project.org/doc/manuals/R-admin.html Installation and administration] Additional reading * [http://cran.r-project.org/manuals.html Manuals] * [http://cran.r-project.org/faqs.html FAQ] * [http://wiki.r-project.org/ Wiki] * [http://www.r-project.org/doc/bib/R-books.html Books] == Installation == First obtain R from one of the [http://cran.r-project.org/mirrors.html CRAN mirrors]. Or alternatively use one of the following links: * [http://lib.stat.cmu.edu/R/CRAN/bin/windows/base/release.htm Base for wintendo] * [http://lib.stat.cmu.edu/R/CRAN/bin/linux/ Linux] * [http://lib.stat.cmu.edu/R/CRAN/bin/macosx/ OS-X] Windows and Mac users most likely want the precompiled binaries listed above, not the source code. The sources have to be compiled before you can use them. If you do not know what this means, you probably do not want to do it! * [http://lib.stat.cmu.edu/R/CRAN/src/base/R-latest.tar.gz Source code] Then follow the instructions in: * [http://lib.stat.cmu.edu/R/CRAN/doc/manuals/R-admin.html#Installing-R-under-Windows Windows] * [http://lib.stat.cmu.edu/R/CRAN/doc/manuals/R-admin.html#Installing-R-under-Mac-OS-X OS-X] * [http://lib.stat.cmu.edu/R/CRAN/doc/manuals/R-admin.html#Installing-R-under-Unix-alikes Proper *NIX] == Using R == Probably the coolest ''feature'' in R is its object oriented design: almost everything is an object in ''R''. Hierarchy, operator/function overcharge and OOP in general is highly and elegantly used, thus if you are familiar with OO languages you'll have a lot of fun. === Package management === R is upgradeable via third-party packages. This packages can be updated/delete ''a la'' perl. That is, packages can be downloaded and installed from within R. First set the option CRAN to your nearest CRAN mirror using chooseCRANmirror(). Then download and install packages pkg1 and pkg2 by > install.packages(c("pkg1", "pkg2")) The essential dependencies of the specified packages will also be fetched. Unless the library is specified (argument lib) the first library in the library search path is used: if this is not writable, R will ask the user (in an interactive session) if the default user library should be created, and if allowed to will install the packages there. If you want to fetch a package and all those it depends on that are not already installed, use e.g. > install.packages("Rcmdr", dependencies = TRUE) In case you want to compile packages yourself use > install.packages(c("pkg1",...), type="source") Removing packages is easy as well, from a running R process they can be removed by > remove.packages(c("pkg1", "pkg2"), lib = file.path("path", "to", "library")) The command <tt>update.packages()</tt> is the simplest way to ensure that all the packages on your system are up to date. * [http://lib.stat.cmu.edu/R/CRAN/doc/manuals/R-admin.html#Add-on-packages More information on package installation] === Data structures === There are several different structures in R namely: '''Numbers''' : 1,2,3,5,8 ... '''Vectors''' : myvec <- c(1,2,3) '''Matrices''' : x <- array(1:20, dim=c(4,5)) '''or''' x <- matrix(c(1:20),4,5) '''Lists''' : Lst <- list(name="Fred", wife="Mary", no.children=3, child.ages=c(4,7,9)) '''Tables''' and '''Matrices''' are different structures and cannot be indistinctively used. Individual elements of an array, matrix or list can be accessed in a C-like way: Thus for the examples above the individual elements can be accessed as: myvec<nowiki>[[2]]</nowiki> and is the number 2 x<nowiki>[3,2]</nowiki> and is the number 7 Lst$name is the same as Lst<nowiki>[[1]]</nowiki> and is the string "Fred", Lst$wife is the same as Lst<nowiki>[[2]]</nowiki> and is the string "Mary", Lst$child.ages<nowiki>[1]</nowiki> is the same as Lst<nowiki>[[4]][1]</nowiki> and is the number 4. == Reading a file == Say you have a file ''ufsr.plot'', which is a two column file then you might want to read it as filename="ufsr.plot" mytable <- read.table(filename,header=FALSE) myvec1 <- mytable<nowiki>[[1]]</nowiki> myvec2 <- mytable<nowiki>[[2]]</nowiki> or alternatively a=matrix(scan(filename,what=0),200,200,byrow=TRUE) == Examples == == Emacs Speaks Statistics == For emacs junkies. This package provides highlighting and other cool interfaces to R (and other statistical analysis packages) * [http://ess.r-project.org/ ESS] [[Category:Analysis]] [[Category:Statistics]] [[Category:Python]] 52e25617a8aacd1ac3505c2175f5df85ca84b918 75 72 2008-06-30T19:43:15Z Orbeckst 7 wikitext text/x-wiki [http://www.r-project.org/ R] (also known as the '''R project''') is a free software environment and language for statistical computing and graphics. It compiles and runs on a wide variety of UNIX platforms, Windows and MacOS. ''R'' is a free implementation of the statistical programming language ''S'' and ''S-Plus'' developed at Bell labs on the 80-90s. It is object oriented and provides several tools for statistical analysis, however it can be used for data manipulation, calculation and graphical display as well. Notably, it can be used from [[python]] using '''[[rpy]]''' which makes all R functions available to python. == Documentation == Essential reading * [http://cran.r-project.org/doc/manuals/R-intro.html An introduction to R] * [http://cran.r-project.org/doc/manuals/R-admin.html Installation and administration] Additional reading * [http://cran.r-project.org/manuals.html Manuals] * [http://cran.r-project.org/faqs.html FAQ] * [http://wiki.r-project.org/ Wiki] * [http://www.r-project.org/doc/bib/R-books.html Books] == Installation == First obtain R from one of the [http://cran.r-project.org/mirrors.html CRAN mirrors]. Or alternatively use one of the following links: * [http://lib.stat.cmu.edu/R/CRAN/bin/windows/base/release.htm Base for wintendo] * [http://lib.stat.cmu.edu/R/CRAN/bin/linux/ Linux] * [http://lib.stat.cmu.edu/R/CRAN/bin/macosx/ OS-X] Windows and Mac users most likely want the precompiled binaries listed above, not the source code. The sources have to be compiled before you can use them. If you do not know what this means, you probably do not want to do it! * [http://lib.stat.cmu.edu/R/CRAN/src/base/R-latest.tar.gz Source code] Then follow the instructions in: * [http://lib.stat.cmu.edu/R/CRAN/doc/manuals/R-admin.html#Installing-R-under-Windows Windows] * [http://lib.stat.cmu.edu/R/CRAN/doc/manuals/R-admin.html#Installing-R-under-Mac-OS-X OS-X] * [http://lib.stat.cmu.edu/R/CRAN/doc/manuals/R-admin.html#Installing-R-under-Unix-alikes Proper *NIX] == Using R == Probably the coolest ''feature'' in R is its object oriented design: almost everything is an object in ''R''. Hierarchy, operator/function overcharge and OOP in general is highly and elegantly used, thus if you are familiar with OO languages you'll have a lot of fun. === Package management === R is upgradeable via third-party packages. This packages can be updated/delete ''a la'' perl. That is, packages can be downloaded and installed from within R. First set the option CRAN to your nearest CRAN mirror using chooseCRANmirror(). Then download and install packages pkg1 and pkg2 by > install.packages(c("pkg1", "pkg2")) The essential dependencies of the specified packages will also be fetched. Unless the library is specified (argument lib) the first library in the library search path is used: if this is not writable, R will ask the user (in an interactive session) if the default user library should be created, and if allowed to will install the packages there. If you want to fetch a package and all those it depends on that are not already installed, use e.g. > install.packages("Rcmdr", dependencies = TRUE) In case you want to compile packages yourself use > install.packages(c("pkg1",...), type="source") Removing packages is easy as well, from a running R process they can be removed by > remove.packages(c("pkg1", "pkg2"), lib = file.path("path", "to", "library")) The command <tt>update.packages()</tt> is the simplest way to ensure that all the packages on your system are up to date. * [http://lib.stat.cmu.edu/R/CRAN/doc/manuals/R-admin.html#Add-on-packages More information on package installation] === Data structures === There are several different structures in R namely: '''Numbers''' : 1,2,3,5,8 ... '''Vectors''' : myvec <- c(1,2,3) '''Matrices''' : x <- array(1:20, dim=c(4,5)) '''or''' x <- matrix(c(1:20),4,5) '''Lists''' : Lst <- list(name="Fred", wife="Mary", no.children=3, child.ages=c(4,7,9)) '''Tables''' and '''Matrices''' are different structures and cannot be indistinctively used. Individual elements of an array, matrix or list can be accessed in a C-like way: Thus for the examples above the individual elements can be accessed as: myvec<nowiki>[[2]]</nowiki> and is the number 2 x<nowiki>[3,2]</nowiki> and is the number 7 Lst$name is the same as Lst<nowiki>[[1]]</nowiki> and is the string "Fred", Lst$wife is the same as Lst<nowiki>[[2]]</nowiki> and is the string "Mary", Lst$child.ages<nowiki>[1]</nowiki> is the same as Lst<nowiki>[[4]][1]</nowiki> and is the number 4. == Reading a file == Say you have a file ''ufsr.plot'', which is a two column file then you might want to read it as filename="ufsr.plot" mytable <- read.table(filename,header=FALSE) myvec1 <- mytable<nowiki>[[1]]</nowiki> myvec2 <- mytable<nowiki>[[2]]</nowiki> or alternatively a=matrix(scan(filename,what=0),200,200,byrow=TRUE) == Examples == == Emacs Speaks Statistics == For emacs junkies. This package provides highlighting and other cool interfaces to R (and other statistical analysis packages) * [http://ess.r-project.org/ ESS] [[Category:Analysis]] [[Category:Statistics]] [[Category:Python]] [[Category:Software]] 254c4762922e3e8df72ba2f34ca623d89d1e8a2e 0 32 73 2008-06-30T19:41:32Z Orbeckst 7 from Woolf Wiki wikitext text/x-wiki [http://rpy.sourceforge.net/ rpy] is a [[python]] interface to the statistics package [[R]]. * [http://rpy.sourceforge.net/documentation.html Documentation] * [http://www2.warwick.ac.uk/fac/sci/moac/currentstudents/peter_cock/python/lin_reg/ Using Python (and R) to calculate Linear Regressions] An example to plot a [http://www.sciencemag.org/cgi/content/full/319/5871/1772 heat map], based on a very nice [http://www2.warwick.ac.uk/fac/sci/moac/currentstudents/peter_cock/python/heatmap/#Python example of how to use R from python to draw a heat map from micro array data]. <python>from rpy import r import numpy data = numpy.random.randn(100,30) # fake data r.X11() # use windowing system X11 r.heatmap(a) </python> [[Image:Hm_gauss2.png|thumb|Example heat map from a Gaussian (mean=0, sd=1) 100x30 matrix of fake data.]] Using an appropriate output device (pdf, png, ...) one can directly produce publication-quality images: <python>r.library('gplots') # loads a library for heatmap.2 r.pdf('hm_gauss2.pdf') # output to file r.heatmap_2(a,col=r.topo_colors(100),trace="none") # plot heatmap r.dev_off() # close file output </python> dcebb6f7b7197e5f209c76274b586d6b2ceda013 74 73 2008-06-30T19:42:43Z Orbeckst 7 wikitext text/x-wiki [http://rpy.sourceforge.net/ rpy] is a [[python]] interface to the statistics package [[R]]. * [http://rpy.sourceforge.net/documentation.html Documentation] * [http://www2.warwick.ac.uk/fac/sci/moac/currentstudents/peter_cock/python/lin_reg/ Using Python (and R) to calculate Linear Regressions] An example to plot a [http://www.sciencemag.org/cgi/content/full/319/5871/1772 heat map], based on a very nice [http://www2.warwick.ac.uk/fac/sci/moac/currentstudents/peter_cock/python/heatmap/#Python example of how to use R from python to draw a heat map from micro array data]. <python>from rpy import r import numpy data = numpy.random.randn(100,30) # fake data r.X11() # use windowing system X11 r.heatmap(a) </python> [[Image:Hm_gauss2.png|thumb|Example heat map from a Gaussian (mean=0, sd=1) 100x30 matrix of fake data.]] Using an appropriate output device (pdf, png, ...) one can directly produce publication-quality images: <python>r.library('gplots') # loads a library for heatmap.2 r.pdf('hm_gauss2.pdf') # output to file r.heatmap_2(a,col=r.topo_colors(100),trace="none") # plot heatmap r.dev_off() # close file output </python> [[Category:Analysis]] [[Category:Statistics]] [[Category:Python]] 27f8839a9ca52620f36bb07c1e43a07aaa186b23 14 33 76 2008-06-30T19:44:46Z Orbeckst 7 New page: Articles about statistical analysis. wikitext text/x-wiki Articles about statistical analysis. edf259a0f6d0e4c38bcd681e25a6eaab8591cc34 14 34 77 2008-06-30T19:45:38Z Orbeckst 7 New page: [[python]] is a versatile scripting language, and hence it is a preferred tool for many tasks, especially [[analysis]] of MD simulations. wikitext text/x-wiki [[python]] is a versatile scripting language, and hence it is a preferred tool for many tasks, especially [[analysis]] of MD simulations. b9ce3509a963421ad963bdd066cc70297303f655 2 35 78 2008-06-30T19:47:04Z Orbeckst 7 Redirecting to [[User:Oliver]] wikitext text/x-wiki #REDIRECT [[User:Oliver]] e1da6deba5a8e1b4ef522d9118d9c58d3cedc9cb 0 36 79 2008-06-30T20:06:51Z Orbeckst 7 basic Amber stuff (mostly from Amber homepage) wikitext text/x-wiki '''[http://amber.scripps.edu/ Amber]''' (Assisted Model Building with Energy Refinement) refers to two things: a set of [http://amber.scripps.edu/#ff molecular mechanical force fields] for the simulation of biomolecules <cite>Ponder2003,Cheatham2001</cite> (which are in the public domain, and are used in a variety of simulation programs); and a [http://amber.scripps.edu/#code package of molecular simulation programs] <cite>Case2005</cite> which includes source code and demos. The current version of the code is Amber version 10, which is distributed by UCSF subject to a [http://amber.scripps.edu/#obtain licensing agreement]. Amber is now distributed in two parts: [http://amber.scripps.edu/#AmberTools AmberTools] and [http://amber.scripps.edu/#Amber10 Amber10]. You can use AmberTools without Amber10, but not vice versa. == Documentation == == Tutorials == * [http://amber.scripps.edu/tutorials/ Beginners' and Advanced Tutorials] == References == <biblio> #Case2005 pmid=16200636 #Ponder2003 pmid=14631816 #Cheatham2001 pmid=11754338 </biblio> 9684e8f7b8cd6c708312713e66b35f7f9a20545d 0 37 80 2008-06-30T20:58:53Z Orbeckst 7 basic Gromacs stuff + refs (uff) wikitext text/x-wiki '''[http://www.gromacs.org/ Gromacs]''' <cite>Berendsen1995, Lindahl2001, vanderSpoel2005, Hess2008</cite> is a MD package developed in Groningen, Netherlands, which is published under the [http://www.gnu.org/copyleft/gpl.html GNU Public license]. It's [http://www.gromacs.org/features/index.php claim to fame] is * raw speed (due to hand coded assembly inner loops and a few optimisations) * extensive collection of analysis tools * coded in C Most force fields can be used, though it only comes natively with Gromos96 (ffG43, ffG53), OPLS-AA, Encad, and the ''deprecated'' Gromacs FF ("ffgmx" &ndash; don't use it!). The Charmm FF has also been ported. Gromacs is fairly easy to install and for Macs it is [http://pdb.finkproject.org/pdb/search.php?summary=gromacs contained] in the [http://fink.sourceforge.net/ Fink] distribution. == Documentation == Gromacs comes with quite extensive [http://www.gromacs.org/content/view/13/27/ documentation] (accessible through their home page). Especially helpful are * [http://www.gromacs.org/component/option,com_wrapper/Itemid,192/ Online Reference] manual * [http://wiki.gromacs.org/ Gromacs Wiki] * [http://www.gromacs.org/content/view/161/203/ Mailinglist archives] == Tutorials == * [http://www.gromacs.org/content/view/137/182/ Gromacs tutorials] * [http://www.alchemistry.org/wiki/index.php/Gromacs_Tutorials Free energy calculations] with Gromacs (from [http://www.alchemistry.org alchemistry.org]) * See also the <tt>share/tutor</tt> directory of the Gromacs distribution == References == <biblio> #Berendsen1995 H. J. C. Berendsen, D. van der Spoel, and R. van Drunen. <i>GROMACS: A message-passing parallel molecular dynamics implementation.</i> Comp. Phys. Comm., 91:43–56, 1995 #Lindahl2001 Erik Lindahl, Berk Hess, and David van der Spoel. <i>Gromacs 3.0: A package for molecular simulation and trajectory analysis.</i> J. Mol. Mod., 7(8):306–317, 2001. doi:[http://dx.doi.org/10.1007/s008940100045 10.1007/s008940100045]. #vanderSpoel2005 pmid=16211538 #Kutzner2007 pmid=17405124 #Hess2008 B. Hess, C. Kutzner, D. van der Spoel, and E. Lindahl. <i>GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation.</i> J. Chem. Theo. Comp., 4(3):435–447, Feb 2008. doi:[http://dx.doi.org/10.1021/ct700301q 10.1021/ct700301q]. </biblio> [[Category:Gromacs]] [[Category:Software]] 93481167178520af3a4bd7b425c40112dd5f323c 81 80 2008-06-30T21:00:31Z Orbeckst 7 /* References */ wikitext text/x-wiki '''[http://www.gromacs.org/ Gromacs]''' <cite>Berendsen1995, Lindahl2001, vanderSpoel2005, Hess2008</cite> is a MD package developed in Groningen, Netherlands, which is published under the [http://www.gnu.org/copyleft/gpl.html GNU Public license]. It's [http://www.gromacs.org/features/index.php claim to fame] is * raw speed (due to hand coded assembly inner loops and a few optimisations) * extensive collection of analysis tools * coded in C Most force fields can be used, though it only comes natively with Gromos96 (ffG43, ffG53), OPLS-AA, Encad, and the ''deprecated'' Gromacs FF ("ffgmx" &ndash; don't use it!). The Charmm FF has also been ported. Gromacs is fairly easy to install and for Macs it is [http://pdb.finkproject.org/pdb/search.php?summary=gromacs contained] in the [http://fink.sourceforge.net/ Fink] distribution. == Documentation == Gromacs comes with quite extensive [http://www.gromacs.org/content/view/13/27/ documentation] (accessible through their home page). Especially helpful are * [http://www.gromacs.org/component/option,com_wrapper/Itemid,192/ Online Reference] manual * [http://wiki.gromacs.org/ Gromacs Wiki] * [http://www.gromacs.org/content/view/161/203/ Mailinglist archives] == Tutorials == * [http://www.gromacs.org/content/view/137/182/ Gromacs tutorials] * [http://www.alchemistry.org/wiki/index.php/Gromacs_Tutorials Free energy calculations] with Gromacs (from [http://www.alchemistry.org alchemistry.org]) * See also the <tt>share/tutor</tt> directory of the Gromacs distribution == References == <biblio> #Berendsen1995 H. J. C. Berendsen, D. van der Spoel, and R. van Drunen. <i>GROMACS: A message-passing parallel molecular dynamics implementation.</i> Comp. Phys. Comm., 91:43–56, 1995. #Lindahl2001 Erik Lindahl, Berk Hess, and David van der Spoel. <i>Gromacs 3.0: A package for molecular simulation and trajectory analysis.</i> J. Mol. Mod., 7(8):306–317, 2001. doi:[http://dx.doi.org/10.1007/s008940100045 10.1007/s008940100045]. #vanderSpoel2005 pmid=16211538 #Kutzner2007 pmid=17405124 #Hess2008 B. Hess, C. Kutzner, D. van der Spoel, and E. Lindahl. <i>GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation.</i> J. Chem. Theo. Comp., 4(3):435–447, Feb 2008. doi:[http://dx.doi.org/10.1021/ct700301q 10.1021/ct700301q]. </biblio> [[Category:Gromacs]] [[Category:Software]] 19b932c8d92c68923a78b15915e4224870a0820e 12 11 82 45 2008-07-01T12:44:48Z Oliver 2 /* The Wiki */ wikitext text/x-wiki == The ''biowerkzeug'' community == The ''biowerkzeug'' community site consists of the '''[http://wiki.biowerkzeug.org biowerkzeug Wiki]''' at [http://wiki.biowerkzeug.org/ wiki.biowerkzeug.org] (which you are reading right now) and the '''[http://forum.biowerkzeug.org/ biowerkzeug Forum]''' at [http://forum.biowerkzeug.org/ forum.biowerkzeug.org]. They were created as a place for users of the [[Hippo]] software and other biomolecular software packages to share ideas and help each other. Furthermore, developers frequent the sites as well and can add their insights and learn what the community wants to see implemented or fixed. == The Wiki == Anyone can read, search and browse the Wiki. Anyone who [[Special:Userlogin|registered]] and verified themselves with a valid email address may edit pages. See '''[[Help:Editing|Editing help]]''' to learn how to do this. If you have used [http://www.mediawiki.org MediaWiki] before then you may still want to have a look at the [[Help:Editing|Editing help]] page to see which additional extensions are enabled on this wiki. As a registered user you can also set up your own "home page" (click on your name to edit it) or change your [[Special:Preferences|Preferences]]. For instance, you can allow other members to send you emails through the wiki or you can customize the way the wiki works. [[Category:Help]] 2e3b7a3885d79a9c95c91e95cd27834e8f503310 86 82 2008-07-01T13:01:47Z Oliver 2 problems? wikitext text/x-wiki == The ''biowerkzeug'' community == The ''biowerkzeug'' community site consists of the '''[http://wiki.biowerkzeug.org biowerkzeug Wiki]''' at [http://wiki.biowerkzeug.org/ wiki.biowerkzeug.org] (which you are reading right now) and the '''[http://forum.biowerkzeug.org/ biowerkzeug Forum]''' at [http://forum.biowerkzeug.org/ forum.biowerkzeug.org]. They were created as a place for users of the [[Hippo]] software and other biomolecular software packages to share ideas and help each other. Furthermore, developers frequent the sites as well and can add their insights and learn what the community wants to see implemented or fixed. == The Wiki == Anyone can read, search and browse the Wiki. Anyone who [[Special:Userlogin|registered]] and verified themselves with a valid email address may edit pages. See '''[[Help:Editing|Editing help]]''' to learn how to do this. If you have used [http://www.mediawiki.org MediaWiki] before then you may still want to have a look at the [[Help:Editing|Editing help]] page to see which additional extensions are enabled on this wiki. As a registered user you can also set up your own "home page" (click on your name to edit it) or change your [[Special:Preferences|Preferences]]. For instance, you can allow other members to send you emails through the wiki or you can customize the way the wiki works. == Problems? == * If you have problems with the Wiki or the Forum then post a question in the [http://forum.biowerkzeug.org/ Forum]. * Comments on particular Wiki pages? Make the heard on the ''''discussion''' page that exists for each Wiki page: click the ''discussion'' link in the top menu bar. [[Category:Help]] 68aed0686527aacebb736d86376fca9c6bbf6804 87 86 2008-07-01T13:02:33Z Oliver 2 /* Problems? */ wikitext text/x-wiki == The ''biowerkzeug'' community == The ''biowerkzeug'' community site consists of the '''[http://wiki.biowerkzeug.org biowerkzeug Wiki]''' at [http://wiki.biowerkzeug.org/ wiki.biowerkzeug.org] (which you are reading right now) and the '''[http://forum.biowerkzeug.org/ biowerkzeug Forum]''' at [http://forum.biowerkzeug.org/ forum.biowerkzeug.org]. They were created as a place for users of the [[Hippo]] software and other biomolecular software packages to share ideas and help each other. Furthermore, developers frequent the sites as well and can add their insights and learn what the community wants to see implemented or fixed. == The Wiki == Anyone can read, search and browse the Wiki. Anyone who [[Special:Userlogin|registered]] and verified themselves with a valid email address may edit pages. See '''[[Help:Editing|Editing help]]''' to learn how to do this. If you have used [http://www.mediawiki.org MediaWiki] before then you may still want to have a look at the [[Help:Editing|Editing help]] page to see which additional extensions are enabled on this wiki. As a registered user you can also set up your own "home page" (click on your name to edit it) or change your [[Special:Preferences|Preferences]]. For instance, you can allow other members to send you emails through the wiki or you can customize the way the wiki works. == Problems? == * If you have problems with the Wiki or the Forum then post a question in the [http://forums.biowerkzeug.org/ Forum]. * Comments on particular Wiki pages? Make the heard on the ''''discussion''' page that exists for each Wiki page: click the ''discussion'' link in the top menu bar. [[Category:Help]] 6e787bf554d9e5db7dcb815326de255ff28a4062 88 87 2008-07-01T13:02:55Z Oliver 2 corrected forums URL wikitext text/x-wiki == The ''biowerkzeug'' community == The ''biowerkzeug'' community site consists of the '''[http://wiki.biowerkzeug.org biowerkzeug Wiki]''' at [http://wiki.biowerkzeug.org/ wiki.biowerkzeug.org] (which you are reading right now) and the '''[http://forum.biowerkzeug.org/ biowerkzeug Forum]''' at [http://forums.biowerkzeug.org/ forums.biowerkzeug.org]. They were created as a place for users of the [[Hippo]] software and other biomolecular software packages to share ideas and help each other. Furthermore, developers frequent the sites as well and can add their insights and learn what the community wants to see implemented or fixed. == The Wiki == Anyone can read, search and browse the Wiki. Anyone who [[Special:Userlogin|registered]] and verified themselves with a valid email address may edit pages. See '''[[Help:Editing|Editing help]]''' to learn how to do this. If you have used [http://www.mediawiki.org MediaWiki] before then you may still want to have a look at the [[Help:Editing|Editing help]] page to see which additional extensions are enabled on this wiki. As a registered user you can also set up your own "home page" (click on your name to edit it) or change your [[Special:Preferences|Preferences]]. For instance, you can allow other members to send you emails through the wiki or you can customize the way the wiki works. == Problems? == * If you have problems with the Wiki or the Forum then post a question in the [http://forums.biowerkzeug.org/ Forum]. * Comments on particular Wiki pages? Make the heard on the ''''discussion''' page that exists for each Wiki page: click the ''discussion'' link in the top menu bar. [[Category:Help]] 5f0c093aec3fb3967144ea46b93d03ba99a76475 89 88 2008-07-01T13:29:03Z Oliver 2 /* Problems? */ link to Forum Wiki -> Bugs wikitext text/x-wiki == The ''biowerkzeug'' community == The ''biowerkzeug'' community site consists of the '''[http://wiki.biowerkzeug.org biowerkzeug Wiki]''' at [http://wiki.biowerkzeug.org/ wiki.biowerkzeug.org] (which you are reading right now) and the '''[http://forum.biowerkzeug.org/ biowerkzeug Forum]''' at [http://forums.biowerkzeug.org/ forums.biowerkzeug.org]. They were created as a place for users of the [[Hippo]] software and other biomolecular software packages to share ideas and help each other. Furthermore, developers frequent the sites as well and can add their insights and learn what the community wants to see implemented or fixed. == The Wiki == Anyone can read, search and browse the Wiki. Anyone who [[Special:Userlogin|registered]] and verified themselves with a valid email address may edit pages. See '''[[Help:Editing|Editing help]]''' to learn how to do this. If you have used [http://www.mediawiki.org MediaWiki] before then you may still want to have a look at the [[Help:Editing|Editing help]] page to see which additional extensions are enabled on this wiki. As a registered user you can also set up your own "home page" (click on your name to edit it) or change your [[Special:Preferences|Preferences]]. For instance, you can allow other members to send you emails through the wiki or you can customize the way the wiki works. == Problems? == * If you have problems with the Wiki then post a question in the [http://forums.biowerkzeug.org/ Forum] under '''[http://forums.biowerkzeug.org/viewforum.php?f=5 Wiki &rarr; Bugs]'''. * Comments on particular Wiki pages? Make the heard on the ''''discussion''' page that exists for each Wiki page: click the ''discussion'' link in the top menu bar. [[Category:Help]] 522d4edadc2e6da6aa7cfdc7f07142ded883c5f8 90 89 2008-07-01T16:38:09Z Oliver 2 /* Problems? */ wikitext text/x-wiki == The ''biowerkzeug'' community == The ''biowerkzeug'' community site consists of the '''[http://wiki.biowerkzeug.org biowerkzeug Wiki]''' at [http://wiki.biowerkzeug.org/ wiki.biowerkzeug.org] (which you are reading right now) and the '''[http://forum.biowerkzeug.org/ biowerkzeug Forum]''' at [http://forums.biowerkzeug.org/ forums.biowerkzeug.org]. They were created as a place for users of the [[Hippo]] software and other biomolecular software packages to share ideas and help each other. Furthermore, developers frequent the sites as well and can add their insights and learn what the community wants to see implemented or fixed. == The Wiki == Anyone can read, search and browse the Wiki. Anyone who [[Special:Userlogin|registered]] and verified themselves with a valid email address may edit pages. See '''[[Help:Editing|Editing help]]''' to learn how to do this. If you have used [http://www.mediawiki.org MediaWiki] before then you may still want to have a look at the [[Help:Editing|Editing help]] page to see which additional extensions are enabled on this wiki. As a registered user you can also set up your own "home page" (click on your name to edit it) or change your [[Special:Preferences|Preferences]]. For instance, you can allow other members to send you emails through the wiki or you can customize the way the wiki works. == Problems? == * If you have problems with the Wiki then post a question in the [http://forums.biowerkzeug.org/ Forum] under '''[http://forums.biowerkzeug.org/viewforum.php?f=5 biowerkzeug community &rarr; Wiki &rarr; Bugs]'''. * Comments on particular Wiki pages? Make the heard on the ''''discussion''' page that exists for each Wiki page: click the ''discussion'' link in the top menu bar. [[Category:Help]] 53103744ed71f0f69e0287a53666700854abbc28 91 90 2008-07-01T16:39:58Z Oliver 2 /* Problems? */ sign name wikitext text/x-wiki == The ''biowerkzeug'' community == The ''biowerkzeug'' community site consists of the '''[http://wiki.biowerkzeug.org biowerkzeug Wiki]''' at [http://wiki.biowerkzeug.org/ wiki.biowerkzeug.org] (which you are reading right now) and the '''[http://forum.biowerkzeug.org/ biowerkzeug Forum]''' at [http://forums.biowerkzeug.org/ forums.biowerkzeug.org]. They were created as a place for users of the [[Hippo]] software and other biomolecular software packages to share ideas and help each other. Furthermore, developers frequent the sites as well and can add their insights and learn what the community wants to see implemented or fixed. == The Wiki == Anyone can read, search and browse the Wiki. Anyone who [[Special:Userlogin|registered]] and verified themselves with a valid email address may edit pages. See '''[[Help:Editing|Editing help]]''' to learn how to do this. If you have used [http://www.mediawiki.org MediaWiki] before then you may still want to have a look at the [[Help:Editing|Editing help]] page to see which additional extensions are enabled on this wiki. As a registered user you can also set up your own "home page" (click on your name to edit it) or change your [[Special:Preferences|Preferences]]. For instance, you can allow other members to send you emails through the wiki or you can customize the way the wiki works. == Problems? == * If you have problems with the Wiki then post a question in the [http://forums.biowerkzeug.org/ Forum] under '''[http://forums.biowerkzeug.org/viewforum.php?f=5 biowerkzeug community &rarr; Wiki &rarr; Bugs]'''. * Comments on particular Wiki pages? Make them heard on the ''''discussion''' page that exists for each Wiki page: click the ''discussion'' link in the top menu bar. Sign the question with your name. (Hint: simply add <tt><nowiki>-- ~~~~</nowiki></tt> to automagicaly insert your name.) [[Category:Help]] 7c74c9997aae8ff9fc5891ff4d62b7fe552b20a6 92 91 2008-07-01T16:40:18Z Oliver 2 /* Problems? */ wikitext text/x-wiki == The ''biowerkzeug'' community == The ''biowerkzeug'' community site consists of the '''[http://wiki.biowerkzeug.org biowerkzeug Wiki]''' at [http://wiki.biowerkzeug.org/ wiki.biowerkzeug.org] (which you are reading right now) and the '''[http://forum.biowerkzeug.org/ biowerkzeug Forum]''' at [http://forums.biowerkzeug.org/ forums.biowerkzeug.org]. They were created as a place for users of the [[Hippo]] software and other biomolecular software packages to share ideas and help each other. Furthermore, developers frequent the sites as well and can add their insights and learn what the community wants to see implemented or fixed. == The Wiki == Anyone can read, search and browse the Wiki. Anyone who [[Special:Userlogin|registered]] and verified themselves with a valid email address may edit pages. See '''[[Help:Editing|Editing help]]''' to learn how to do this. If you have used [http://www.mediawiki.org MediaWiki] before then you may still want to have a look at the [[Help:Editing|Editing help]] page to see which additional extensions are enabled on this wiki. As a registered user you can also set up your own "home page" (click on your name to edit it) or change your [[Special:Preferences|Preferences]]. For instance, you can allow other members to send you emails through the wiki or you can customize the way the wiki works. == Problems? == * If you have problems with the Wiki then post a question in the [http://forums.biowerkzeug.org/ Forum] under '''[http://forums.biowerkzeug.org/viewforum.php?f=5 biowerkzeug community &rarr; Wiki &rarr; Bugs]'''. * Comments on particular Wiki pages? Make them heard on the ''''discussion''' page that exists for each Wiki page: click the ''discussion'' link in the top menu bar. Sign the question with your name. (Hint: simply add "<tt><nowiki>-- ~~~~</nowiki></tt>" to automagicaly insert your name.) [[Category:Help]] e659566efafe092e7c6426e6c82be3ec7efca739 13 38 83 2008-07-01T12:48:45Z Oliver 2 /* Missing features */ stuff advertised in Help but not working (yet) wikitext text/x-wiki == Missing features == * Syntax highlighting not working yet. * GNUplot not working yet. * Upload not working yet. * Inline images from external links not working. &mdash; [[User:Oliver|Oli]] 6f1265ca6390242873a84f8a7db53859268c001a 84 83 2008-07-01T12:49:00Z Oliver 2 /* Missing features */ sig wikitext text/x-wiki == Missing features == * Syntax highlighting not working yet. * GNUplot not working yet. * Upload not working yet. * Inline images from external links not working. &mdash; [[User:Oliver|Oli]] 12:49, 1 July 2008 (UTC) 9163325ad1986e6a6e0689792dedf48a5fac7af5 12 7 85 34 2008-07-01T12:58:05Z Oliver 2 /* Categories */ more details + formatting wikitext text/x-wiki This page should tell you how to work with this Wiki &ndash; it's not complicated, promise! (In fact, the whole point of a wiki is to make it as easy for the user as possible to document whatever there is worth documenting). ==Editing an existing page== # Select the ''Edit'' link at the top. # Type or simply copy and paste text, eg from your editor, shell, or an email, and use the ''preview'' button. # Once it looks sort-of right commit your changes by clicking ''save page''. The Media Wiki page has a comprehensive list of the [http://meta.wikipedia.org/wiki/MediaWiki_User%27s_Guide:_Editing_overview#The_wiki_markup Wiki markup] but you can also look at the code of existing pages (edit the page but don't save it) or use the formatting buttons at the top of your editing box. The most important thing is just to put something on the page and not to worry too much about formatting. If in doubt simply leave one initial space and everything gets formatted verbatim; anything resembling an URL will be turned into a link (or enclose it in <nowiki>'[' and ']'</nowiki>). ==Editing a new page== If you click on a red link then you enter a non-existing page. This is not bad: Simply start editing it and ''write it yourself''. You can't make mistakes. Just do it. ==Creating a new page== To make a non-existing page you simply insert the link into an existing page, it appears in red, you click it and then edit it. == Signing your name == Sometimes this is useful: three tildes <nowiki>~~~</nowiki> signs your name like this: [[User:Oliver|Oliver]]; four <nowiki>~~~~</nowiki> dates it too: [[User:Oliver|Oliver]] 18:32, 24 January 2006 (EST) == Categories == [http://meta.wikimedia.org/wiki/Help:Category '''Categories''' in MediaWiki] provide automatic indexes that are useful as tables of contents. See the Special Page '''[[Special:Categories]]''' for a list of all defined categories. * You '''define a category''' by adding one or more special tags at the end of a page: add <tt><nowiki>[[</nowiki>Category:''Category name''<nowiki>]]</nowiki></tt> to the page's wikitext source. For instance, add to page that describes analysis scripts for Charmm <nowiki>[[Category:Charmm]]</nowiki> <nowiki>[[Category:Analysis]]</nowiki> : as the last two lines. This will implicitly define the categories [[:Category:Analysis]] and [[:Category:Charmm]]. * The '''category pages''' can also be edited. In addition, the wiki software adds an alphabetically sorted list of all pages in the category. This makes a category useful as an entry point into a subject. ** One ''must'' edit a category page for the wiki to create the indexed list (even if it is just an empty edit). ** It is also possible to add another category to a category page: This will turn this category in a subcategory on the other category page. * In order to '''reference a category within a page as a normal wiki link''' (without adding the page to the category) prefix the link name with a colon. For example: <tt><nowiki>[[:</nowiki>Category:Analysis<nowiki>]]</nowiki></tt>. == Page maintenance == === Redirection === A 'symbolic link' to another pages is created with the [http://meta.wikimedia.org/wiki/Help:Redirection REDIRECT] command: <nowiki>#REDIRECT [[</nowiki>''page''<nowiki>]]</nowiki> ==Highlighting sourcecode== Wikimedia can do syntax highlighting for over a dozen programming languages, including c, python, perl, fortran, and c++. Just surround the code with a tag of the name of the language. For example: <pre> <python> import re lines = file("ifconf.log").readlines() l_iter = iter(lines) nodes = [] for l in l_iter: if l[:7] == "compute": node = l.split('.')[0] temp = l_iter.next().split() iface, addr = temp[0], temp[4] nodes.append([node, iface, addr]) </python> </pre> Gives you <python> import re lines = file("ifconf.log").readlines() l_iter = iter(lines) nodes = [] for l in l_iter: if l[:7] == "compute": node = l.split('.')[0] temp = l_iter.next().split() iface, addr = temp[0], temp[4] nodes.append([node, iface, addr]) </python> ==Inserting Gnuplot graphs== You can insert gnuplot graphs directly into mediawiki by using the <tt>gnuplot</tt> tag. For example: <pre> <gnuplot> set output 'func_approx.png' plot '-' using 1:2 t 'quadratic approximation' with linesp lt 1 lw 3, \ '-' using 1:2 t 'cubic approximation' with linesp lt 2 lw 3 1 2 2 4 3 8 4 16 e 1 3 2 9 3 27 4 81 e </gnuplot> </pre> Gives you the following: <gnuplot> set output 'func_approx.png' plot '-' using 1:2 t 'quadratic approximation' with linesp lt 1 lw 3, \ '-' using 1:2 t 'cubic approximation' with linesp lt 2 lw 3 1 2 2 4 3 8 4 16 e 1 3 2 9 3 27 4 81 e </gnuplot> == Adding bibliographic references (specifically [http://www.pubmed.gov PubMed]) == You can insert bibliographic references into pages by using the <tt><nowiki><cite></nowiki></tt> and <tt><nowiki><biblio></nowiki></tt> tags. This uses the PubMed id number (pmid) found at the bottom of the abstract listing for a particular article. Mediawiki will go to [http://www.pubmed.gov PubMed] and pull the citation information for the reference. Using the key in front of the pmid assignment within the <tt><nowiki><cite></nowiki></tt> tag (see example below) gives you a reference to the article within the current page. For example, although you can obmit the pmid and simply format the reference yourself. <pre> Recent papers from the Woolf lab <cite>jcp2005 proteins2005 jcp2004</cite>: ===Bibliography=== <biblio> #jcp2005 pmid=15847458 #proteins2005 pmid=15828005 #jcp2004 pmid=15634036 </biblio> </pre> Will give you this: Recent papers from the Woolf lab <cite>jcp2005 proteins2005 jcp2004</cite>: <b>Bibliography</b> <biblio> #jcp2005 pmid=15847458 #proteins2005 pmid=15828005 #jcp2004 pmid=15634036 </biblio> == Images == [[Image:NAChR M2 water.jpg|200px|right]] The following shows two methods of how to incorporate an image in a wiki page. === Upload === The image is uploaded to the webserver and resides in the wiki (somewhere... you don't need to know where, it's a secret) # first [[Special:Upload|upload]] it (use the link in the toolbox on the left) # enter a wiki link such as <tt><nowiki>[[Image:NAChR M2 water.jpg|200px]] </nowiki></tt> into the text An exhaustive description of the image capabilities are discussed in the [http://en.wikipedia.org/wiki/Wikipedia:Extended_image_syntax Wikipedia Extended Image Syntax]. Most importantly, if you want to change the size of the image, add a size option <tt>|''size''px</tt> option (<tt>|200px</tt> in the example above). The new version of MediaWiki gives you a plethora of options to add captions, float the image to left or right, change sizes, show it as a (fast) thumbnail, ... === Web link === Alternatively, just put in a link to a png or jpg such as <tt><nowiki>http://sbcb.bioch.ox.ac.uk/oliver/Priv/USA/California/goldenpoppy.png</nowiki></tt>: http://sbcb.bioch.ox.ac.uk/oliver/Priv/USA/California/goldenpoppy.png The image appears in its original size. == Links == If you want to gain an in-depth knowledge of working with this Wiki then have a look at these links: === Wikipedia edit help documents === * Wikipedia's [http://en.wikipedia.org/wiki/Wikipedia:How_to_edit_a_page full listing of wiki editing commands] (make sure you come back here to edit... otherwise you will be editing Wikipedia) * Wikipedia [http://en.wikipedia.org/wiki/Wikipedia:Extended_image_syntax Extended Image Syntax] for all your image inclusion needs * Syntax of [http://en.wikipedia.org/wiki/Help:Table Table] commands === MediaWiki documents === The [http://wiki.biowerkzeug.org/ Biowerkzeug Wiki] uses the [http://www.mediawiki.org/wiki MediaWiki] software. For more on MediaWiki see the following links: * [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] * [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list] * [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ] * [http://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list] [[Category:Help]] 83e6cd788e57c0566842aba3717b55d741e0f79e 4 15 93 47 2008-07-02T00:21:22Z Oliver 2 /* The biowerkzeug community sites */ fixed forum link wikitext text/x-wiki == The ''biowerkzeug'' community sites == The ''biowerkzeug'' community site consists of the '''[http://wiki.biowerkzeug.org biowerkzeug Wiki]''' at [http://wiki.biowerkzeug.org/ wiki.biowerkzeug.org] (which you are reading right now) and the '''[http://forums.biowerkzeug.org/ biowerkzeug Forum]''' at [http://forums.biowerkzeug.org/ forums.biowerkzeug.org]. They were created as a place for users of the [[Hippo]] software and other biomolecular software packages to share ideas and help each other. Furthermore, developers frequent the sites as well and can add their insights and learn what the community wants to see implemented or fixed. The ''biowerkzeug'' community websites (the Forum and the Wiki) are managed by [http://www.biowerkzeug.com/about.php Biowerkzeug, Ltd]. == The name == ''biowerkzeug'' is German and translates to ''bio-tool''. [[Category:Help]] 6c31d0437b385df19ebfff84f295004f69c8cf46 0 39 95 2008-08-06T15:40:00Z Martin 5 New page: = OPLS = To convert between HIPPO and GROMACS units use this excel sheet wikitext text/x-wiki = OPLS = To convert between HIPPO and GROMACS units use this excel sheet 35e755b4d8d0c798bd71441bb9c96ec14f000dff 0 40 96 2008-10-02T20:56:00Z Oliver 2 stub (taken from manual) + embellished wikitext text/x-wiki '''Hippo''' is a software package for simulation and analysis of bio-molecules at an atomic level. It has been specifically developed for very efficient protein folding studies in aqueous and membrane environments. The code is very fast due to optimized and hand-coded assembly routines which make use of fast multi-media instructions on modern x86 cpus. Hippo is (partially) parallelized (using industry-standard [http://www.openmp.org/ openMP]). == Download == Binaries will be publicly available from the [http://www.biowerkzeug.com/ Biowerkzeg.com download page] for '''Linux''', '''Windows''', and '''Mac OS X (Intel platform only)'''. For immediate access to beta-versions please email ''martin''-AT-''ulmschneider.com''. == Features == === Simulation methods === * [[Molecular dynamics]] (MD) in NVT, NPT, NVE ensembles * Metropolis [[Monte Carlo]] (MC) in NVT and NPT ensembles <cite>JACS2004,JPhysChemB2006</cite> * [[Replica exchange]] with MD and MC === Force fields === * OPLS-AA <cite>Jorgensen1996,Kaminski2001</cite> === Solvation models === * explicit solvent (water: TIP4P <cite>Jorgensen1985</cite>, SPC <cite>Berendsen1981</cite>) * Generalized Born implicit solvent (GB/SA) * Generalized Born implicit membrane (GB/IM) <cite>Proteins2007,BJ2007,Proteins2005</cite> === Enhanced productivity === A number of features make it easy to use Hippo so that one can spend more time on working on problems and less time on setting up structures or dealing with system crashes: * seamless restarts * intelligent pdb structure loader: reads most pdbs, can complete missing atoms, and builds the topology === Analysis === A growing number of analysis tools are built into Hippo, for instance * adiabatic translation+rotation energy scan (to determine the Generalized Born energy of a peptide in a membrane) <cite>MMB2008,BJ2006</cite> * RMSD * helicity The output format is a standard pdb-movie; thus many other analysis tools can also be used. == References == <biblio> #MMB2008 pmid=18428040 #Proteins2007 pmid=17600830 #BJ2007 pmid=17218457 #BJ2006 pmid=16339877 #JPhysChemB2006 pmid=16913813 #Proteins2005 pmid=15723347 #JACS2004 pmid=14871118 #Kaminski2001 George A. Kaminski, Richard A. Friesner, Julian Tirado-Rives, and William L. Jorgensen. ''Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides''. J. Phys. Chem. B, 105(28):6474–6487, 2001. [http://dx.doi.org/10.1021/jp003919d 10.1021/jp003919d]. #Jorgensen1996 W. L. Jorgensen, D. S. Maxwell, and J. Tirado-Rives. ''Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids''. J. Am. Chem. Soc., 118(45):11225–11236, 1996. [http://dx.doi.org/10.1021/ja9621760 10.1021/ja9621760]. #Jorgensen1985 W. L. Jorgensen and J. D. Madura. ''Temperature and size dependence for Monte-Carlo simulations of TIP4P water''. Mol. Phys., 56(6):1381–1392, December 1985. #Berendsen1981 H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, and J. Hermans. ''Interaction models for water in relation to protein hydration''. In B. Pullman, editor, Intermolecular Forces, page 331. D. Reidel Publishing Company, Dordrecht, Holland, 1981. </biblio> 987dfb5ca6d250abd2513324a40098324a65025b 99 96 2008-10-03T09:44:22Z Oliver 2 /* References */ SWINK wikitext text/x-wiki '''Hippo''' is a software package for simulation and analysis of bio-molecules at an atomic level. It has been specifically developed for very efficient protein folding studies in aqueous and membrane environments. The code is very fast due to optimized and hand-coded assembly routines which make use of fast multi-media instructions on modern x86 cpus. Hippo is (partially) parallelized (using industry-standard [http://www.openmp.org/ openMP]). == Download == Binaries will be publicly available from the [http://www.biowerkzeug.com/ Biowerkzeg.com download page] for '''Linux''', '''Windows''', and '''Mac OS X (Intel platform only)'''. For immediate access to beta-versions please email ''martin''-AT-''ulmschneider.com''. == Features == === Simulation methods === * [[Molecular dynamics]] (MD) in NVT, NPT, NVE ensembles * Metropolis [[Monte Carlo]] (MC) in NVT and NPT ensembles <cite>JACS2004,JPhysChemB2006</cite> * [[Replica exchange]] with MD and MC === Force fields === * OPLS-AA <cite>Jorgensen1996,Kaminski2001</cite> === Solvation models === * explicit solvent (water: TIP4P <cite>Jorgensen1985</cite>, SPC <cite>Berendsen1981</cite>) * Generalized Born implicit solvent (GB/SA) * Generalized Born implicit membrane (GB/IM) <cite>Proteins2007,BJ2007,Proteins2005</cite> === Enhanced productivity === A number of features make it easy to use Hippo so that one can spend more time on working on problems and less time on setting up structures or dealing with system crashes: * seamless restarts * intelligent pdb structure loader: reads most pdbs, can complete missing atoms, and builds the topology === Analysis === A growing number of analysis tools are built into Hippo, for instance * adiabatic translation+rotation energy scan (to determine the Generalized Born energy of a peptide in a membrane) <cite>MMB2008,BJ2006</cite> * RMSD * helicity The output format is a standard pdb-movie; thus many other analysis tools can also be used. == References == <biblio> #MMB2008 pmid=18428040 #Proteins2007 pmid=17600830 #BJ2007 pmid=17218457 #BJ2006 pmid=16339877 #JPhysChemB2006 pmid=16913813 #Proteins2005 pmid=15723347 #JACS2004 pmid=14871118 #Kaminski2001 George A. Kaminski, Richard A. Friesner, Julian Tirado-Rives, and William L. Jorgensen. ''Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides''. J. Phys. Chem. B, 105(28):6474–6487, 2001. [http://dx.doi.org/10.1021/jp003919d 10.1021/jp003919d]. #Jorgensen1996 W. L. Jorgensen, D. S. Maxwell, and J. Tirado-Rives. ''Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids''. J. Am. Chem. Soc., 118(45):11225–11236, 1996. [http://dx.doi.org/10.1021/ja9621760 10.1021/ja9621760]. #Jorgensen1985 W. L. Jorgensen and J. D. Madura. ''Temperature and size dependence for Monte-Carlo simulations of TIP4P water''. Mol. Phys., 56(6):1381–1392, December 1985. #Berendsen1981 H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, and J. Hermans. ''Interaction models for water in relation to protein hydration''. In B. Pullman, editor, Intermolecular Forces, page 331. D. Reidel Publishing Company, Dordrecht, Holland, 1981. #Cordes2002 pmid=12417206 </biblio> bd2c390aa65a721c652ce9912908133b26af4316 100 99 2008-10-03T10:10:49Z Oliver 2 /* References */ Daura paper (but Wiley are total wackos - who in their right mind uses greater and smaller signs in a DOI?? Use http://www.w3schools.com/tags/ref_urlencode.asp to encode the entities. wikitext text/x-wiki '''Hippo''' is a software package for simulation and analysis of bio-molecules at an atomic level. It has been specifically developed for very efficient protein folding studies in aqueous and membrane environments. The code is very fast due to optimized and hand-coded assembly routines which make use of fast multi-media instructions on modern x86 cpus. Hippo is (partially) parallelized (using industry-standard [http://www.openmp.org/ openMP]). == Download == Binaries will be publicly available from the [http://www.biowerkzeug.com/ Biowerkzeg.com download page] for '''Linux''', '''Windows''', and '''Mac OS X (Intel platform only)'''. For immediate access to beta-versions please email ''martin''-AT-''ulmschneider.com''. == Features == === Simulation methods === * [[Molecular dynamics]] (MD) in NVT, NPT, NVE ensembles * Metropolis [[Monte Carlo]] (MC) in NVT and NPT ensembles <cite>JACS2004,JPhysChemB2006</cite> * [[Replica exchange]] with MD and MC === Force fields === * OPLS-AA <cite>Jorgensen1996,Kaminski2001</cite> === Solvation models === * explicit solvent (water: TIP4P <cite>Jorgensen1985</cite>, SPC <cite>Berendsen1981</cite>) * Generalized Born implicit solvent (GB/SA) * Generalized Born implicit membrane (GB/IM) <cite>Proteins2007,BJ2007,Proteins2005</cite> === Enhanced productivity === A number of features make it easy to use Hippo so that one can spend more time on working on problems and less time on setting up structures or dealing with system crashes: * seamless restarts * intelligent pdb structure loader: reads most pdbs, can complete missing atoms, and builds the topology === Analysis === A growing number of analysis tools are built into Hippo, for instance * adiabatic translation+rotation energy scan (to determine the Generalized Born energy of a peptide in a membrane) <cite>MMB2008,BJ2006</cite> * RMSD * helicity The output format is a standard pdb-movie; thus many other analysis tools can also be used. == References == <biblio> #MMB2008 pmid=18428040 #Proteins2007 pmid=17600830 #BJ2007 pmid=17218457 #BJ2006 pmid=16339877 #JPhysChemB2006 pmid=16913813 #Proteins2005 pmid=15723347 #JACS2004 pmid=14871118 #Kaminski2001 George A. Kaminski, Richard A. Friesner, Julian Tirado-Rives, and William L. Jorgensen. ''Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides''. J. Phys. Chem. B, 105(28):6474–6487, 2001. [http://dx.doi.org/10.1021/jp003919d 10.1021/jp003919d]. #Jorgensen1996 W. L. Jorgensen, D. S. Maxwell, and J. Tirado-Rives. ''Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids''. J. Am. Chem. Soc., 118(45):11225–11236, 1996. [http://dx.doi.org/10.1021/ja9621760 10.1021/ja9621760]. #Jorgensen1985 W. L. Jorgensen and J. D. Madura. ''Temperature and size dependence for Monte-Carlo simulations of TIP4P water''. Mol. Phys., 56(6):1381–1392, December 1985. #Berendsen1981 H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, and J. Hermans. ''Interaction models for water in relation to protein hydration''. In B. Pullman, editor, Intermolecular Forces, page 331. D. Reidel Publishing Company, Dordrecht, Holland, 1981. #Cordes2002 pmid=12417206 #Daura1999 X Daura, K Gademann, B Jaun, D Seebach, WF van Gunsteren, and AE Mark. ''Peptide folding: When simulation meets experiment''. Angewandte Chemie-International Edition, 38 (1-2):236–240, 1999. [http://dx.doi.org/10.1002/(SICI)1521-3773(19990115)38:1/2%3C236::AID-ANIE236%3E3.0.CO;2-M <nowiki>10.1002/(SICI)1521-3773(19990115)38:1/2<236::AID-ANIE236>3.0.CO;2-M</nowiki>]. </biblio> d8debbccef70ff4d7751d3e8e0eee50c479ccd03 0 40 101 100 2008-10-03T10:14:18Z Oliver 2 /* Analysis */ added other analysis tools (from manual) + references wikitext text/x-wiki '''Hippo''' is a software package for simulation and analysis of bio-molecules at an atomic level. It has been specifically developed for very efficient protein folding studies in aqueous and membrane environments. The code is very fast due to optimized and hand-coded assembly routines which make use of fast multi-media instructions on modern x86 cpus. Hippo is (partially) parallelized (using industry-standard [http://www.openmp.org/ openMP]). == Download == Binaries will be publicly available from the [http://www.biowerkzeug.com/ Biowerkzeg.com download page] for '''Linux''', '''Windows''', and '''Mac OS X (Intel platform only)'''. For immediate access to beta-versions please email ''martin''-AT-''ulmschneider.com''. == Features == === Simulation methods === * [[Molecular dynamics]] (MD) in NVT, NPT, NVE ensembles * Metropolis [[Monte Carlo]] (MC) in NVT and NPT ensembles <cite>JACS2004,JPhysChemB2006</cite> * [[Replica exchange]] with MD and MC === Force fields === * OPLS-AA <cite>Jorgensen1996,Kaminski2001</cite> === Solvation models === * explicit solvent (water: TIP4P <cite>Jorgensen1985</cite>, SPC <cite>Berendsen1981</cite>) * Generalized Born implicit solvent (GB/SA) * Generalized Born implicit membrane (GB/IM) <cite>Proteins2007,BJ2007,Proteins2005</cite> === Enhanced productivity === A number of features make it easy to use Hippo so that one can spend more time on working on problems and less time on setting up structures or dealing with system crashes: * seamless restarts * intelligent pdb structure loader: reads most pdbs, can complete missing atoms, and builds the topology === Analysis === A growing number of analysis tools are built into Hippo, for instance ; adiabatic translation+rotation energy scan: determines the Generalized Born energy of a peptide in a membrane <cite>MMB2008,BJ2006</cite>; this allows to decide if a (typically helical) peptide inserts into the membrane and at which depth and angle or if it prefers a surface-bound or even a fully solvated state ; RMSD: calculates the [[RMSD|root mean square deviation]] of trajectory frames to a reference structure ; helicity: degree of helicity of segments along trajectory ; Z - tilt - kink graph: Calculates center of mass, tilt angle, and kink angle of a peptide in a membrane as a function of simulation time. The membrane is in the xy plane, with z = 0 the membrane center. Kink angle is with respect to the membrane normal. <cite>Cordes2002</cite> ; cluster: Performs a cluster analysis using the pairwise method by Daura et al.<cite>Daura1999</cite> ; fit to phase: recenters trajectory on the centre of mass of a phase (such as a lipid membrane) ; fit solute to previous frames: Generate a PDB movie by RMSD fitting the solute of each frame to the previous frame. The Hippo output format is a xyz-movie; thus many other [[analysis]] tools can also be used. == References == <biblio> #MMB2008 pmid=18428040 #Proteins2007 pmid=17600830 #BJ2007 pmid=17218457 #BJ2006 pmid=16339877 #JPhysChemB2006 pmid=16913813 #Proteins2005 pmid=15723347 #JACS2004 pmid=14871118 #Kaminski2001 George A. Kaminski, Richard A. Friesner, Julian Tirado-Rives, and William L. Jorgensen. ''Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides''. J. Phys. Chem. B, 105(28):6474–6487, 2001. [http://dx.doi.org/10.1021/jp003919d 10.1021/jp003919d]. #Jorgensen1996 W. L. Jorgensen, D. S. Maxwell, and J. Tirado-Rives. ''Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids''. J. Am. Chem. Soc., 118(45):11225–11236, 1996. [http://dx.doi.org/10.1021/ja9621760 10.1021/ja9621760]. #Jorgensen1985 W. L. Jorgensen and J. D. Madura. ''Temperature and size dependence for Monte-Carlo simulations of TIP4P water''. Mol. Phys., 56(6):1381–1392, December 1985. #Berendsen1981 H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, and J. Hermans. ''Interaction models for water in relation to protein hydration''. In B. Pullman, editor, Intermolecular Forces, page 331. D. Reidel Publishing Company, Dordrecht, Holland, 1981. #Cordes2002 pmid=12417206 #Daura1999 X Daura, K Gademann, B Jaun, D Seebach, WF van Gunsteren, and AE Mark. ''Peptide folding: When simulation meets experiment''. Angewandte Chemie-International Edition, 38 (1-2):236–240, 1999. [http://dx.doi.org/10.1002/(SICI)1521-3773(19990115)38:1/2%3C236::AID-ANIE236%3E3.0.CO;2-M <nowiki>10.1002/(SICI)1521-3773(19990115)38:1/2<236::AID-ANIE236>3.0.CO;2-M</nowiki>]. </biblio> c01a1abcabd95a149492519cdd6abf390f139d17 103 101 2008-10-03T10:25:51Z Oliver 2 /* Analysis */ peptidescan picture wikitext text/x-wiki '''Hippo''' is a software package for simulation and analysis of bio-molecules at an atomic level. It has been specifically developed for very efficient protein folding studies in aqueous and membrane environments. The code is very fast due to optimized and hand-coded assembly routines which make use of fast multi-media instructions on modern x86 cpus. Hippo is (partially) parallelized (using industry-standard [http://www.openmp.org/ openMP]). == Download == Binaries will be publicly available from the [http://www.biowerkzeug.com/ Biowerkzeg.com download page] for '''Linux''', '''Windows''', and '''Mac OS X (Intel platform only)'''. For immediate access to beta-versions please email ''martin''-AT-''ulmschneider.com''. == Features == === Simulation methods === * [[Molecular dynamics]] (MD) in NVT, NPT, NVE ensembles * Metropolis [[Monte Carlo]] (MC) in NVT and NPT ensembles <cite>JACS2004,JPhysChemB2006</cite> * [[Replica exchange]] with MD and MC === Force fields === * OPLS-AA <cite>Jorgensen1996,Kaminski2001</cite> === Solvation models === * explicit solvent (water: TIP4P <cite>Jorgensen1985</cite>, SPC <cite>Berendsen1981</cite>) * Generalized Born implicit solvent (GB/SA) * Generalized Born implicit membrane (GB/IM) <cite>Proteins2007,BJ2007,Proteins2005</cite> === Enhanced productivity === A number of features make it easy to use Hippo so that one can spend more time on working on problems and less time on setting up structures or dealing with system crashes: * seamless restarts * intelligent pdb structure loader: reads most pdbs, can complete missing atoms, and builds the topology === Analysis === [[Image:Peptidescan.jpg|thumb|right|Adiabatic free energy surface for different positions and orientations of a helical peptide in a membrane (output from the ''translation+rotation energy scan'' analysis tool).]] A growing number of analysis tools are built into Hippo, for instance ; adiabatic translation+rotation energy scan: determines the Generalized Born energy of a peptide in a membrane <cite>MMB2008,BJ2006</cite>; this allows to decide if a (typically helical) peptide inserts into the membrane and at which depth and angle or if it prefers a surface-bound or even a fully solvated state ; RMSD: calculates the [[RMSD|root mean square deviation]] of trajectory frames to a reference structure ; helicity: degree of helicity of segments along trajectory ; Z - tilt - kink graph: Calculates center of mass, tilt angle, and kink angle of a peptide in a membrane as a function of simulation time. The membrane is in the xy plane, with z = 0 the membrane center. Kink angle is with respect to the membrane normal. <cite>Cordes2002</cite> ; cluster: Performs a cluster analysis using the pairwise method by Daura et al.<cite>Daura1999</cite> ; fit to phase: recenters trajectory on the centre of mass of a phase (such as a lipid membrane) ; fit solute to previous frames: Generate a PDB movie by RMSD fitting the solute of each frame to the previous frame. The Hippo output format is a xyz-movie; thus many other [[analysis]] tools can also be used. == References == <biblio> #MMB2008 pmid=18428040 #Proteins2007 pmid=17600830 #BJ2007 pmid=17218457 #BJ2006 pmid=16339877 #JPhysChemB2006 pmid=16913813 #Proteins2005 pmid=15723347 #JACS2004 pmid=14871118 #Kaminski2001 George A. Kaminski, Richard A. Friesner, Julian Tirado-Rives, and William L. Jorgensen. ''Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides''. J. Phys. Chem. B, 105(28):6474–6487, 2001. [http://dx.doi.org/10.1021/jp003919d 10.1021/jp003919d]. #Jorgensen1996 W. L. Jorgensen, D. S. Maxwell, and J. Tirado-Rives. ''Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids''. J. Am. Chem. Soc., 118(45):11225–11236, 1996. [http://dx.doi.org/10.1021/ja9621760 10.1021/ja9621760]. #Jorgensen1985 W. L. Jorgensen and J. D. Madura. ''Temperature and size dependence for Monte-Carlo simulations of TIP4P water''. Mol. Phys., 56(6):1381–1392, December 1985. #Berendsen1981 H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, and J. Hermans. ''Interaction models for water in relation to protein hydration''. In B. Pullman, editor, Intermolecular Forces, page 331. D. Reidel Publishing Company, Dordrecht, Holland, 1981. #Cordes2002 pmid=12417206 #Daura1999 X Daura, K Gademann, B Jaun, D Seebach, WF van Gunsteren, and AE Mark. ''Peptide folding: When simulation meets experiment''. Angewandte Chemie-International Edition, 38 (1-2):236–240, 1999. [http://dx.doi.org/10.1002/(SICI)1521-3773(19990115)38:1/2%3C236::AID-ANIE236%3E3.0.CO;2-M <nowiki>10.1002/(SICI)1521-3773(19990115)38:1/2<236::AID-ANIE236>3.0.CO;2-M</nowiki>]. </biblio> 67237c2818e28a198b8fb5c2b2a9967919a83453 104 103 2008-10-03T10:27:17Z Oliver 2 /* Analysis */ wikitext text/x-wiki '''Hippo''' is a software package for simulation and analysis of bio-molecules at an atomic level. It has been specifically developed for very efficient protein folding studies in aqueous and membrane environments. The code is very fast due to optimized and hand-coded assembly routines which make use of fast multi-media instructions on modern x86 cpus. Hippo is (partially) parallelized (using industry-standard [http://www.openmp.org/ openMP]). == Download == Binaries will be publicly available from the [http://www.biowerkzeug.com/ Biowerkzeg.com download page] for '''Linux''', '''Windows''', and '''Mac OS X (Intel platform only)'''. For immediate access to beta-versions please email ''martin''-AT-''ulmschneider.com''. == Features == === Simulation methods === * [[Molecular dynamics]] (MD) in NVT, NPT, NVE ensembles * Metropolis [[Monte Carlo]] (MC) in NVT and NPT ensembles <cite>JACS2004,JPhysChemB2006</cite> * [[Replica exchange]] with MD and MC === Force fields === * OPLS-AA <cite>Jorgensen1996,Kaminski2001</cite> === Solvation models === * explicit solvent (water: TIP4P <cite>Jorgensen1985</cite>, SPC <cite>Berendsen1981</cite>) * Generalized Born implicit solvent (GB/SA) * Generalized Born implicit membrane (GB/IM) <cite>Proteins2007,BJ2007,Proteins2005</cite> === Enhanced productivity === A number of features make it easy to use Hippo so that one can spend more time on working on problems and less time on setting up structures or dealing with system crashes: * seamless restarts * intelligent pdb structure loader: reads most pdbs, can complete missing atoms, and builds the topology === Analysis === [[Image:Peptidescan.jpg|thumb|right|Adiabatic Generalized Born energy surface for different positions and orientations of a helical peptide in a membrane (output from the ''translation+rotation energy scan'' analysis tool).]] A growing number of analysis tools are built into Hippo, for instance ; adiabatic translation+rotation energy scan: determines the Generalized Born energy of a peptide in a membrane <cite>MMB2008,BJ2006</cite>; this allows to decide if a (typically helical) peptide inserts into the membrane and at which depth and angle or if it prefers a surface-bound or even a fully solvated state ; RMSD: calculates the [[RMSD|root mean square deviation]] of trajectory frames to a reference structure ; helicity: degree of helicity of segments along trajectory ; Z - tilt - kink graph: Calculates center of mass, tilt angle, and kink angle of a peptide in a membrane as a function of simulation time. The membrane is in the xy plane, with z = 0 the membrane center. Kink angle is with respect to the membrane normal. <cite>Cordes2002</cite> ; cluster: Performs a cluster analysis using the pairwise method by Daura et al.<cite>Daura1999</cite> ; fit to phase: recenters trajectory on the centre of mass of a phase (such as a lipid membrane) ; fit solute to previous frames: Generate a PDB movie by RMSD fitting the solute of each frame to the previous frame. The Hippo output format is a xyz-movie; thus many other [[analysis]] tools can also be used. == References == <biblio> #MMB2008 pmid=18428040 #Proteins2007 pmid=17600830 #BJ2007 pmid=17218457 #BJ2006 pmid=16339877 #JPhysChemB2006 pmid=16913813 #Proteins2005 pmid=15723347 #JACS2004 pmid=14871118 #Kaminski2001 George A. Kaminski, Richard A. Friesner, Julian Tirado-Rives, and William L. Jorgensen. ''Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides''. J. Phys. Chem. B, 105(28):6474–6487, 2001. [http://dx.doi.org/10.1021/jp003919d 10.1021/jp003919d]. #Jorgensen1996 W. L. Jorgensen, D. S. Maxwell, and J. Tirado-Rives. ''Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids''. J. Am. Chem. Soc., 118(45):11225–11236, 1996. [http://dx.doi.org/10.1021/ja9621760 10.1021/ja9621760]. #Jorgensen1985 W. L. Jorgensen and J. D. Madura. ''Temperature and size dependence for Monte-Carlo simulations of TIP4P water''. Mol. Phys., 56(6):1381–1392, December 1985. #Berendsen1981 H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, and J. Hermans. ''Interaction models for water in relation to protein hydration''. In B. Pullman, editor, Intermolecular Forces, page 331. D. Reidel Publishing Company, Dordrecht, Holland, 1981. #Cordes2002 pmid=12417206 #Daura1999 X Daura, K Gademann, B Jaun, D Seebach, WF van Gunsteren, and AE Mark. ''Peptide folding: When simulation meets experiment''. Angewandte Chemie-International Edition, 38 (1-2):236–240, 1999. [http://dx.doi.org/10.1002/(SICI)1521-3773(19990115)38:1/2%3C236::AID-ANIE236%3E3.0.CO;2-M <nowiki>10.1002/(SICI)1521-3773(19990115)38:1/2<236::AID-ANIE236>3.0.CO;2-M</nowiki>]. </biblio> 967a37b879048d299c959c7057cb60cec2132eb6 106 104 2008-10-03T10:31:52Z Oliver 2 added folding picture as 'Appetithappen' wikitext text/x-wiki [[Image:Gbim.jpg‎|frame|right|A peptide folds and inserts into a membrane; the membrane is represented by an implicit Generalized Born model.]] '''Hippo''' is a software package for simulation and analysis of bio-molecules at an atomic level. It has been specifically developed for very efficient protein folding studies in aqueous and membrane environments. The code is very fast due to optimized and hand-coded assembly routines which make use of fast multi-media instructions on modern x86 cpus. Hippo is (partially) parallelized (using industry-standard [http://www.openmp.org/ openMP]). == Download == Binaries will be publicly available from the [http://www.biowerkzeug.com/ Biowerkzeg.com download page] for '''Linux''', '''Windows''', and '''Mac OS X (Intel platform only)'''. For immediate access to beta-versions please email ''martin''-AT-''ulmschneider.com''. == Features == === Simulation methods === * [[Molecular dynamics]] (MD) in NVT, NPT, NVE ensembles * Metropolis [[Monte Carlo]] (MC) in NVT and NPT ensembles <cite>JACS2004,JPhysChemB2006</cite> * [[Replica exchange]] with MD and MC === Force fields === * OPLS-AA <cite>Jorgensen1996,Kaminski2001</cite> === Solvation models === * explicit solvent (water: TIP4P <cite>Jorgensen1985</cite>, SPC <cite>Berendsen1981</cite>) * Generalized Born implicit solvent (GB/SA) * Generalized Born implicit membrane (GB/IM) <cite>Proteins2007,BJ2007,Proteins2005</cite> === Enhanced productivity === A number of features make it easy to use Hippo so that one can spend more time on working on problems and less time on setting up structures or dealing with system crashes: * seamless restarts * intelligent pdb structure loader: reads most pdbs, can complete missing atoms, and builds the topology === Analysis === [[Image:Peptidescan.jpg|thumb|right|Adiabatic Generalized Born energy surface for different positions and orientations of a helical peptide in a membrane (output from the ''translation+rotation energy scan'' analysis tool).]] A growing number of analysis tools are built into Hippo, for instance ; adiabatic translation+rotation energy scan: determines the Generalized Born energy of a peptide in a membrane <cite>MMB2008,BJ2006</cite>; this allows to decide if a (typically helical) peptide inserts into the membrane and at which depth and angle or if it prefers a surface-bound or even a fully solvated state ; RMSD: calculates the [[RMSD|root mean square deviation]] of trajectory frames to a reference structure ; helicity: degree of helicity of segments along trajectory ; Z - tilt - kink graph: Calculates center of mass, tilt angle, and kink angle of a peptide in a membrane as a function of simulation time. The membrane is in the xy plane, with z = 0 the membrane center. Kink angle is with respect to the membrane normal. <cite>Cordes2002</cite> ; cluster: Performs a cluster analysis using the pairwise method by Daura et al.<cite>Daura1999</cite> ; fit to phase: recenters trajectory on the centre of mass of a phase (such as a lipid membrane) ; fit solute to previous frames: Generate a PDB movie by RMSD fitting the solute of each frame to the previous frame. The Hippo output format is a xyz-movie; thus many other [[analysis]] tools can also be used. == References == <biblio> #MMB2008 pmid=18428040 #Proteins2007 pmid=17600830 #BJ2007 pmid=17218457 #BJ2006 pmid=16339877 #JPhysChemB2006 pmid=16913813 #Proteins2005 pmid=15723347 #JACS2004 pmid=14871118 #Kaminski2001 George A. Kaminski, Richard A. Friesner, Julian Tirado-Rives, and William L. Jorgensen. ''Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides''. J. Phys. Chem. B, 105(28):6474–6487, 2001. [http://dx.doi.org/10.1021/jp003919d 10.1021/jp003919d]. #Jorgensen1996 W. L. Jorgensen, D. S. Maxwell, and J. Tirado-Rives. ''Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids''. J. Am. Chem. Soc., 118(45):11225–11236, 1996. [http://dx.doi.org/10.1021/ja9621760 10.1021/ja9621760]. #Jorgensen1985 W. L. Jorgensen and J. D. Madura. ''Temperature and size dependence for Monte-Carlo simulations of TIP4P water''. Mol. Phys., 56(6):1381–1392, December 1985. #Berendsen1981 H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, and J. Hermans. ''Interaction models for water in relation to protein hydration''. In B. Pullman, editor, Intermolecular Forces, page 331. D. Reidel Publishing Company, Dordrecht, Holland, 1981. #Cordes2002 pmid=12417206 #Daura1999 X Daura, K Gademann, B Jaun, D Seebach, WF van Gunsteren, and AE Mark. ''Peptide folding: When simulation meets experiment''. Angewandte Chemie-International Edition, 38 (1-2):236–240, 1999. [http://dx.doi.org/10.1002/(SICI)1521-3773(19990115)38:1/2%3C236::AID-ANIE236%3E3.0.CO;2-M <nowiki>10.1002/(SICI)1521-3773(19990115)38:1/2<236::AID-ANIE236>3.0.CO;2-M</nowiki>]. </biblio> 1b618e9ebd73cecca0433d6a978fb75c8c0b097e 107 106 2008-10-03T10:34:12Z Oliver 2 /* Analysis */ wikitext text/x-wiki [[Image:Gbim.jpg‎|frame|right|A peptide folds and inserts into a membrane; the membrane is represented by an implicit Generalized Born model.]] '''Hippo''' is a software package for simulation and analysis of bio-molecules at an atomic level. It has been specifically developed for very efficient protein folding studies in aqueous and membrane environments. The code is very fast due to optimized and hand-coded assembly routines which make use of fast multi-media instructions on modern x86 cpus. Hippo is (partially) parallelized (using industry-standard [http://www.openmp.org/ openMP]). == Download == Binaries will be publicly available from the [http://www.biowerkzeug.com/ Biowerkzeg.com download page] for '''Linux''', '''Windows''', and '''Mac OS X (Intel platform only)'''. For immediate access to beta-versions please email ''martin''-AT-''ulmschneider.com''. == Features == === Simulation methods === * [[Molecular dynamics]] (MD) in NVT, NPT, NVE ensembles * Metropolis [[Monte Carlo]] (MC) in NVT and NPT ensembles <cite>JACS2004,JPhysChemB2006</cite> * [[Replica exchange]] with MD and MC === Force fields === * OPLS-AA <cite>Jorgensen1996,Kaminski2001</cite> === Solvation models === * explicit solvent (water: TIP4P <cite>Jorgensen1985</cite>, SPC <cite>Berendsen1981</cite>) * Generalized Born implicit solvent (GB/SA) * Generalized Born implicit membrane (GB/IM) <cite>Proteins2007,BJ2007,Proteins2005</cite> === Enhanced productivity === A number of features make it easy to use Hippo so that one can spend more time on working on problems and less time on setting up structures or dealing with system crashes: * seamless restarts * intelligent pdb structure loader: reads most pdbs, can complete missing atoms, and builds the topology === Analysis === [[Image:Peptidescan.jpg|frame|right|Adiabatic Generalized Born energy surface for different positions and orientations of a helical peptide in a membrane (output from the ''translation+rotation energy scan'' analysis tool).]] A growing number of analysis tools are built into Hippo, for instance ; adiabatic translation+rotation energy scan: determines the Generalized Born energy of a peptide in a membrane <cite>MMB2008,BJ2006</cite>; this allows to decide if a (typically helical) peptide inserts into the membrane and at which depth and angle or if it prefers a surface-bound or even a fully solvated state ; RMSD: calculates the [[RMSD|root mean square deviation]] of trajectory frames to a reference structure ; helicity: degree of helicity of segments along trajectory ; Z - tilt - kink graph: Calculates center of mass, tilt angle, and kink angle of a peptide in a membrane as a function of simulation time. The membrane is in the xy plane, with z = 0 the membrane center. Kink angle is with respect to the membrane normal. <cite>Cordes2002</cite> ; cluster: Performs a cluster analysis using the pairwise method by Daura et al.<cite>Daura1999</cite> ; fit to phase: recenters trajectory on the centre of mass of a phase (such as a lipid membrane) ; fit solute to previous frames: Generate a PDB movie by RMSD fitting the solute of each frame to the previous frame. The Hippo output format is a xyz-movie; thus many other [[analysis]] tools can also be used. == References == <biblio> #MMB2008 pmid=18428040 #Proteins2007 pmid=17600830 #BJ2007 pmid=17218457 #BJ2006 pmid=16339877 #JPhysChemB2006 pmid=16913813 #Proteins2005 pmid=15723347 #JACS2004 pmid=14871118 #Kaminski2001 George A. Kaminski, Richard A. Friesner, Julian Tirado-Rives, and William L. Jorgensen. ''Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides''. J. Phys. Chem. B, 105(28):6474–6487, 2001. [http://dx.doi.org/10.1021/jp003919d 10.1021/jp003919d]. #Jorgensen1996 W. L. Jorgensen, D. S. Maxwell, and J. Tirado-Rives. ''Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids''. J. Am. Chem. Soc., 118(45):11225–11236, 1996. [http://dx.doi.org/10.1021/ja9621760 10.1021/ja9621760]. #Jorgensen1985 W. L. Jorgensen and J. D. Madura. ''Temperature and size dependence for Monte-Carlo simulations of TIP4P water''. Mol. Phys., 56(6):1381–1392, December 1985. #Berendsen1981 H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, and J. Hermans. ''Interaction models for water in relation to protein hydration''. In B. Pullman, editor, Intermolecular Forces, page 331. D. Reidel Publishing Company, Dordrecht, Holland, 1981. #Cordes2002 pmid=12417206 #Daura1999 X Daura, K Gademann, B Jaun, D Seebach, WF van Gunsteren, and AE Mark. ''Peptide folding: When simulation meets experiment''. Angewandte Chemie-International Edition, 38 (1-2):236–240, 1999. [http://dx.doi.org/10.1002/(SICI)1521-3773(19990115)38:1/2%3C236::AID-ANIE236%3E3.0.CO;2-M <nowiki>10.1002/(SICI)1521-3773(19990115)38:1/2<236::AID-ANIE236>3.0.CO;2-M</nowiki>]. </biblio> f42f92e015f855ce22b193cad555c476ca409533 108 107 2008-10-03T10:39:52Z Oliver 2 /* Analysis */ xyz link wikitext text/x-wiki [[Image:Gbim.jpg‎|frame|right|A peptide folds and inserts into a membrane; the membrane is represented by an implicit Generalized Born model.]] '''Hippo''' is a software package for simulation and analysis of bio-molecules at an atomic level. It has been specifically developed for very efficient protein folding studies in aqueous and membrane environments. The code is very fast due to optimized and hand-coded assembly routines which make use of fast multi-media instructions on modern x86 cpus. Hippo is (partially) parallelized (using industry-standard [http://www.openmp.org/ openMP]). == Download == Binaries will be publicly available from the [http://www.biowerkzeug.com/ Biowerkzeg.com download page] for '''Linux''', '''Windows''', and '''Mac OS X (Intel platform only)'''. For immediate access to beta-versions please email ''martin''-AT-''ulmschneider.com''. == Features == === Simulation methods === * [[Molecular dynamics]] (MD) in NVT, NPT, NVE ensembles * Metropolis [[Monte Carlo]] (MC) in NVT and NPT ensembles <cite>JACS2004,JPhysChemB2006</cite> * [[Replica exchange]] with MD and MC === Force fields === * OPLS-AA <cite>Jorgensen1996,Kaminski2001</cite> === Solvation models === * explicit solvent (water: TIP4P <cite>Jorgensen1985</cite>, SPC <cite>Berendsen1981</cite>) * Generalized Born implicit solvent (GB/SA) * Generalized Born implicit membrane (GB/IM) <cite>Proteins2007,BJ2007,Proteins2005</cite> === Enhanced productivity === A number of features make it easy to use Hippo so that one can spend more time on working on problems and less time on setting up structures or dealing with system crashes: * seamless restarts * intelligent pdb structure loader: reads most pdbs, can complete missing atoms, and builds the topology === Analysis === [[Image:Peptidescan.jpg|frame|right|Adiabatic Generalized Born energy surface for different positions and orientations of a helical peptide in a membrane (output from the ''translation+rotation energy scan'' analysis tool).]] A growing number of analysis tools are built into Hippo, for instance ; adiabatic translation+rotation energy scan: determines the Generalized Born energy of a peptide in a membrane <cite>MMB2008,BJ2006</cite>; this allows to decide if a (typically helical) peptide inserts into the membrane and at which depth and angle or if it prefers a surface-bound or even a fully solvated state ; RMSD: calculates the [[RMSD|root mean square deviation]] of trajectory frames to a reference structure ; helicity: degree of helicity of segments along trajectory ; Z - tilt - kink graph: Calculates center of mass, tilt angle, and kink angle of a peptide in a membrane as a function of simulation time. The membrane is in the xy plane, with z = 0 the membrane center. Kink angle is with respect to the membrane normal. <cite>Cordes2002</cite> ; cluster: Performs a cluster analysis using the pairwise method by Daura et al.<cite>Daura1999</cite> ; fit to phase: recenters trajectory on the centre of mass of a phase (such as a lipid membrane) ; fit solute to previous frames: Generate a PDB movie by RMSD fitting the solute of each frame to the previous frame. The Hippo output format is a binary [[File formats#xyz-movie|xyz-movie]] (see the [http://openbabel.org/wiki/XYZ definition of the xyz format]); thus many other [[analysis]] tools can also be used. == References == <biblio> #MMB2008 pmid=18428040 #Proteins2007 pmid=17600830 #BJ2007 pmid=17218457 #BJ2006 pmid=16339877 #JPhysChemB2006 pmid=16913813 #Proteins2005 pmid=15723347 #JACS2004 pmid=14871118 #Kaminski2001 George A. Kaminski, Richard A. Friesner, Julian Tirado-Rives, and William L. Jorgensen. ''Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides''. J. Phys. Chem. B, 105(28):6474–6487, 2001. [http://dx.doi.org/10.1021/jp003919d 10.1021/jp003919d]. #Jorgensen1996 W. L. Jorgensen, D. S. Maxwell, and J. Tirado-Rives. ''Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids''. J. Am. Chem. Soc., 118(45):11225–11236, 1996. [http://dx.doi.org/10.1021/ja9621760 10.1021/ja9621760]. #Jorgensen1985 W. L. Jorgensen and J. D. Madura. ''Temperature and size dependence for Monte-Carlo simulations of TIP4P water''. Mol. Phys., 56(6):1381–1392, December 1985. #Berendsen1981 H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, and J. Hermans. ''Interaction models for water in relation to protein hydration''. In B. Pullman, editor, Intermolecular Forces, page 331. D. Reidel Publishing Company, Dordrecht, Holland, 1981. #Cordes2002 pmid=12417206 #Daura1999 X Daura, K Gademann, B Jaun, D Seebach, WF van Gunsteren, and AE Mark. ''Peptide folding: When simulation meets experiment''. Angewandte Chemie-International Edition, 38 (1-2):236–240, 1999. [http://dx.doi.org/10.1002/(SICI)1521-3773(19990115)38:1/2%3C236::AID-ANIE236%3E3.0.CO;2-M <nowiki>10.1002/(SICI)1521-3773(19990115)38:1/2<236::AID-ANIE236>3.0.CO;2-M</nowiki>]. </biblio> d5c540cc40cb2561f3b51b56951ae610f789bf93 109 108 2008-10-07T00:51:53Z Oliver 2 /* Enhanced productivity */ graphical frontend wikitext text/x-wiki [[Image:Gbim.jpg‎|frame|right|A peptide folds and inserts into a membrane; the membrane is represented by an implicit Generalized Born model.]] '''Hippo''' is a software package for simulation and analysis of bio-molecules at an atomic level. It has been specifically developed for very efficient protein folding studies in aqueous and membrane environments. The code is very fast due to optimized and hand-coded assembly routines which make use of fast multi-media instructions on modern x86 cpus. Hippo is (partially) parallelized (using industry-standard [http://www.openmp.org/ openMP]). == Download == Binaries will be publicly available from the [http://www.biowerkzeug.com/ Biowerkzeg.com download page] for '''Linux''', '''Windows''', and '''Mac OS X (Intel platform only)'''. For immediate access to beta-versions please email ''martin''-AT-''ulmschneider.com''. == Features == === Simulation methods === * [[Molecular dynamics]] (MD) in NVT, NPT, NVE ensembles * Metropolis [[Monte Carlo]] (MC) in NVT and NPT ensembles <cite>JACS2004,JPhysChemB2006</cite> * [[Replica exchange]] with MD and MC === Force fields === * OPLS-AA <cite>Jorgensen1996,Kaminski2001</cite> === Solvation models === * explicit solvent (water: TIP4P <cite>Jorgensen1985</cite>, SPC <cite>Berendsen1981</cite>) * Generalized Born implicit solvent (GB/SA) * Generalized Born implicit membrane (GB/IM) <cite>Proteins2007,BJ2007,Proteins2005</cite> === Enhanced productivity === A number of features make it easy to use Hippo so that one can spend more time on working on problems and less time on setting up structures or dealing with system crashes: * seamless restarts * intelligent pdb structure loader: reads most pdbs, can complete missing atoms, and builds the topology * graphical frontend under development (Windows only) === Analysis === [[Image:Peptidescan.jpg|frame|right|Adiabatic Generalized Born energy surface for different positions and orientations of a helical peptide in a membrane (output from the ''translation+rotation energy scan'' analysis tool).]] A growing number of analysis tools are built into Hippo, for instance ; adiabatic translation+rotation energy scan: determines the Generalized Born energy of a peptide in a membrane <cite>MMB2008,BJ2006</cite>; this allows to decide if a (typically helical) peptide inserts into the membrane and at which depth and angle or if it prefers a surface-bound or even a fully solvated state ; RMSD: calculates the [[RMSD|root mean square deviation]] of trajectory frames to a reference structure ; helicity: degree of helicity of segments along trajectory ; Z - tilt - kink graph: Calculates center of mass, tilt angle, and kink angle of a peptide in a membrane as a function of simulation time. The membrane is in the xy plane, with z = 0 the membrane center. Kink angle is with respect to the membrane normal. <cite>Cordes2002</cite> ; cluster: Performs a cluster analysis using the pairwise method by Daura et al.<cite>Daura1999</cite> ; fit to phase: recenters trajectory on the centre of mass of a phase (such as a lipid membrane) ; fit solute to previous frames: Generate a PDB movie by RMSD fitting the solute of each frame to the previous frame. The Hippo output format is a binary [[File formats#xyz-movie|xyz-movie]] (see the [http://openbabel.org/wiki/XYZ definition of the xyz format]); thus many other [[analysis]] tools can also be used. == References == <biblio> #MMB2008 pmid=18428040 #Proteins2007 pmid=17600830 #BJ2007 pmid=17218457 #BJ2006 pmid=16339877 #JPhysChemB2006 pmid=16913813 #Proteins2005 pmid=15723347 #JACS2004 pmid=14871118 #Kaminski2001 George A. Kaminski, Richard A. Friesner, Julian Tirado-Rives, and William L. Jorgensen. ''Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides''. J. Phys. Chem. B, 105(28):6474–6487, 2001. [http://dx.doi.org/10.1021/jp003919d 10.1021/jp003919d]. #Jorgensen1996 W. L. Jorgensen, D. S. Maxwell, and J. Tirado-Rives. ''Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids''. J. Am. Chem. Soc., 118(45):11225–11236, 1996. [http://dx.doi.org/10.1021/ja9621760 10.1021/ja9621760]. #Jorgensen1985 W. L. Jorgensen and J. D. Madura. ''Temperature and size dependence for Monte-Carlo simulations of TIP4P water''. Mol. Phys., 56(6):1381–1392, December 1985. #Berendsen1981 H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, and J. Hermans. ''Interaction models for water in relation to protein hydration''. In B. Pullman, editor, Intermolecular Forces, page 331. D. Reidel Publishing Company, Dordrecht, Holland, 1981. #Cordes2002 pmid=12417206 #Daura1999 X Daura, K Gademann, B Jaun, D Seebach, WF van Gunsteren, and AE Mark. ''Peptide folding: When simulation meets experiment''. Angewandte Chemie-International Edition, 38 (1-2):236–240, 1999. [http://dx.doi.org/10.1002/(SICI)1521-3773(19990115)38:1/2%3C236::AID-ANIE236%3E3.0.CO;2-M <nowiki>10.1002/(SICI)1521-3773(19990115)38:1/2<236::AID-ANIE236>3.0.CO;2-M</nowiki>]. </biblio> d92aaba90539658ea979e7463134f28a520cfddd 110 109 2008-10-08T09:16:03Z Oliver 2 categories wikitext text/x-wiki [[Image:Gbim.jpg‎|frame|right|A peptide folds and inserts into a membrane; the membrane is represented by an implicit Generalized Born model.]] '''Hippo''' is a software package for simulation and analysis of bio-molecules at an atomic level. It has been specifically developed for very efficient protein folding studies in aqueous and membrane environments. The code is very fast due to optimized and hand-coded assembly routines which make use of fast multi-media instructions on modern x86 cpus. Hippo is (partially) parallelized (using industry-standard [http://www.openmp.org/ openMP]). == Download == Binaries will be publicly available from the [http://www.biowerkzeug.com/ Biowerkzeg.com download page] for '''Linux''', '''Windows''', and '''Mac OS X (Intel platform only)'''. For immediate access to beta-versions please email ''martin''-AT-''ulmschneider.com''. == Features == === Simulation methods === * [[Molecular dynamics]] (MD) in NVT, NPT, NVE ensembles * Metropolis [[Monte Carlo]] (MC) in NVT and NPT ensembles <cite>JACS2004,JPhysChemB2006</cite> * [[Replica exchange]] with MD and MC === Force fields === * OPLS-AA <cite>Jorgensen1996,Kaminski2001</cite> === Solvation models === * explicit solvent (water: TIP4P <cite>Jorgensen1985</cite>, SPC <cite>Berendsen1981</cite>) * Generalized Born implicit solvent (GB/SA) * Generalized Born implicit membrane (GB/IM) <cite>Proteins2007,BJ2007,Proteins2005</cite> === Enhanced productivity === A number of features make it easy to use Hippo so that one can spend more time on working on problems and less time on setting up structures or dealing with system crashes: * seamless restarts * intelligent pdb structure loader: reads most pdbs, can complete missing atoms, and builds the topology * graphical frontend under development (Windows only) === Analysis === [[Image:Peptidescan.jpg|frame|right|Adiabatic Generalized Born energy surface for different positions and orientations of a helical peptide in a membrane (output from the ''translation+rotation energy scan'' analysis tool).]] A growing number of analysis tools are built into Hippo, for instance ; adiabatic translation+rotation energy scan: determines the Generalized Born energy of a peptide in a membrane <cite>MMB2008,BJ2006</cite>; this allows to decide if a (typically helical) peptide inserts into the membrane and at which depth and angle or if it prefers a surface-bound or even a fully solvated state ; RMSD: calculates the [[RMSD|root mean square deviation]] of trajectory frames to a reference structure ; helicity: degree of helicity of segments along trajectory ; Z - tilt - kink graph: Calculates center of mass, tilt angle, and kink angle of a peptide in a membrane as a function of simulation time. The membrane is in the xy plane, with z = 0 the membrane center. Kink angle is with respect to the membrane normal. <cite>Cordes2002</cite> ; cluster: Performs a cluster analysis using the pairwise method by Daura et al.<cite>Daura1999</cite> ; fit to phase: recenters trajectory on the centre of mass of a phase (such as a lipid membrane) ; fit solute to previous frames: Generate a PDB movie by RMSD fitting the solute of each frame to the previous frame. The Hippo output format is a binary [[File formats#xyz-movie|xyz-movie]] (see the [http://openbabel.org/wiki/XYZ definition of the xyz format]); thus many other [[analysis]] tools can also be used. == References == <biblio> #MMB2008 pmid=18428040 #Proteins2007 pmid=17600830 #BJ2007 pmid=17218457 #BJ2006 pmid=16339877 #JPhysChemB2006 pmid=16913813 #Proteins2005 pmid=15723347 #JACS2004 pmid=14871118 #Kaminski2001 George A. Kaminski, Richard A. Friesner, Julian Tirado-Rives, and William L. Jorgensen. ''Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides''. J. Phys. Chem. B, 105(28):6474–6487, 2001. [http://dx.doi.org/10.1021/jp003919d 10.1021/jp003919d]. #Jorgensen1996 W. L. Jorgensen, D. S. Maxwell, and J. Tirado-Rives. ''Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids''. J. Am. Chem. Soc., 118(45):11225–11236, 1996. [http://dx.doi.org/10.1021/ja9621760 10.1021/ja9621760]. #Jorgensen1985 W. L. Jorgensen and J. D. Madura. ''Temperature and size dependence for Monte-Carlo simulations of TIP4P water''. Mol. Phys., 56(6):1381–1392, December 1985. #Berendsen1981 H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, and J. Hermans. ''Interaction models for water in relation to protein hydration''. In B. Pullman, editor, Intermolecular Forces, page 331. D. Reidel Publishing Company, Dordrecht, Holland, 1981. #Cordes2002 pmid=12417206 #Daura1999 X Daura, K Gademann, B Jaun, D Seebach, WF van Gunsteren, and AE Mark. ''Peptide folding: When simulation meets experiment''. Angewandte Chemie-International Edition, 38 (1-2):236–240, 1999. [http://dx.doi.org/10.1002/(SICI)1521-3773(19990115)38:1/2%3C236::AID-ANIE236%3E3.0.CO;2-M <nowiki>10.1002/(SICI)1521-3773(19990115)38:1/2<236::AID-ANIE236>3.0.CO;2-M</nowiki>]. </biblio> [[Category:Hippo]] [[Category:Software]] 0f649bbc8c3951b63acf474c9b9cad20e8128c14 112 110 2008-10-17T21:38:28Z Orbeckst 7 /* Download */ wikitext text/x-wiki [[Image:Gbim.jpg‎|frame|right|A peptide folds and inserts into a membrane; the membrane is represented by an implicit Generalized Born model.]] '''Hippo''' is a software package for simulation and analysis of bio-molecules at an atomic level. It has been specifically developed for very efficient protein folding studies in aqueous and membrane environments. The code is very fast due to optimized and hand-coded assembly routines which make use of fast multi-media instructions on modern x86 cpus. Hippo is (partially) parallelized (using industry-standard [http://www.openmp.org/ openMP]). == Download == Binaries are publicly available from the [http://www.biowerkzeug.com/ Biowerkzeg.com download page] for '''Linux''' and '''Windows'''. <!-- , and '''Mac OS X (Intel platform only)'''. --> == Installation == Unzip the downloaded file. It will unpack into its own <tt>hippo</tt> directory where you will find * compiled executables (see below) ** <tt>hippo</tt>: the MD and MC program ** <tt>analyse</tt>: the analysis program * the manual ([http://www.biowerkzeug.de/downloads/hippo/hippo_manual.pdf pdf]) * the [[Hippo license|license]] (to which you consent by downloading) * the OPLS-AA forcefield file (in Hippo format) * the readme.txt file * the <tt>testjobs</tt> directory with example systems The package includes binaries that run under Linux and Windows on any Intel or AMD processor that has the SSE or SSSE3 multi media instructions. Depending on your system and needs, choose the following executable from the package: {| |+Hippo executables !cpu !!Linux !!Windows |- |SSSE3 (Core Duo,...) ||<tt>hippo</tt> ||<tt>hippo.exe</tt> |- |SSE (PIII,P4,Athlon,...) ||<tt>hippo_p3</tt> ||<tt>hippo_p3.exe</tt> |} If in doubt, simply try them out in order; if it will not run you will receive an error message such as Fatal Error: This program was not built to run on the processor in your system. The allowed processors are: Intel(R) Core(TM) Duo processors and compatible Intel processors with supplemental Streaming SIMD Extensions 3 (SSSE3) instruction support. In this case try the <tt>hippo_p3</tt> or <tt>hippo_p3.exe</tt> executable. If this still doesn't work, [http://forums.biowerkzeug.org/viewforum.php?f=6 post a request in the Hippo Installation forum]. Executables with the <tt>_mpi</tt> extension have been compiled with OpenMP and can run on multiple CPUs. However, not all code segments are yet parallelized. == Test cases == The <tt>testjobs</tt> directory contains a number of testcases. Run the <tt>calc_testjobs_linux.bat</tt> or <tt>calc_testjobs_win32.bat</tt> script in order to perform ''all'' tests. On modern processors this should take between 2 and 4 Minutes. Use the tests in order to get started in running your own systems. == Features == === Simulation methods === * [[Molecular dynamics]] (MD) in NVT, NPT, NVE ensembles * Metropolis [[Monte Carlo]] (MC) in NVT and NPT ensembles <cite>JACS2004,JPhysChemB2006</cite> * [[Replica exchange]] with MD and MC === Force fields === * OPLS-AA <cite>Jorgensen1996,Kaminski2001</cite> === Solvation models === * explicit solvent (water: TIP4P <cite>Jorgensen1985</cite>, SPC <cite>Berendsen1981</cite>) * Generalized Born implicit solvent (GB/SA) * Generalized Born implicit membrane (GB/IM) <cite>Proteins2007,BJ2007,Proteins2005</cite> === Enhanced productivity === A number of features make it easy to use Hippo so that one can spend more time on working on problems and less time on setting up structures or dealing with system crashes: * seamless restarts * intelligent pdb structure loader: reads most pdbs, can complete missing atoms, and builds the topology * graphical frontend under development (Windows only) === Analysis === [[Image:Peptidescan.jpg|frame|right|Adiabatic Generalized Born energy surface for different positions and orientations of a helical peptide in a membrane (output from the ''translation+rotation energy scan'' analysis tool).]] A growing number of analysis tools are built into Hippo, for instance ; adiabatic translation+rotation energy scan: determines the Generalized Born energy of a peptide in a membrane <cite>MMB2008,BJ2006</cite>; this allows to decide if a (typically helical) peptide inserts into the membrane and at which depth and angle or if it prefers a surface-bound or even a fully solvated state ; RMSD: calculates the [[RMSD|root mean square deviation]] of trajectory frames to a reference structure ; helicity: degree of helicity of segments along trajectory ; Z - tilt - kink graph: Calculates center of mass, tilt angle, and kink angle of a peptide in a membrane as a function of simulation time. The membrane is in the xy plane, with z = 0 the membrane center. Kink angle is with respect to the membrane normal. <cite>Cordes2002</cite> ; cluster: Performs a cluster analysis using the pairwise method by Daura et al.<cite>Daura1999</cite> ; fit to phase: recenters trajectory on the centre of mass of a phase (such as a lipid membrane) ; fit solute to previous frames: Generate a PDB movie by RMSD fitting the solute of each frame to the previous frame. The Hippo output format is a binary [[File formats#xyz-movie|xyz-movie]] (see the [http://openbabel.org/wiki/XYZ definition of the xyz format]); thus many other [[analysis]] tools can also be used. == References == <biblio> #MMB2008 pmid=18428040 #Proteins2007 pmid=17600830 #BJ2007 pmid=17218457 #BJ2006 pmid=16339877 #JPhysChemB2006 pmid=16913813 #Proteins2005 pmid=15723347 #JACS2004 pmid=14871118 #Kaminski2001 George A. Kaminski, Richard A. Friesner, Julian Tirado-Rives, and William L. Jorgensen. ''Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides''. J. Phys. Chem. B, 105(28):6474–6487, 2001. [http://dx.doi.org/10.1021/jp003919d 10.1021/jp003919d]. #Jorgensen1996 W. L. Jorgensen, D. S. Maxwell, and J. Tirado-Rives. ''Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids''. J. Am. Chem. Soc., 118(45):11225–11236, 1996. [http://dx.doi.org/10.1021/ja9621760 10.1021/ja9621760]. #Jorgensen1985 W. L. Jorgensen and J. D. Madura. ''Temperature and size dependence for Monte-Carlo simulations of TIP4P water''. Mol. Phys., 56(6):1381–1392, December 1985. #Berendsen1981 H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, and J. Hermans. ''Interaction models for water in relation to protein hydration''. In B. Pullman, editor, Intermolecular Forces, page 331. D. Reidel Publishing Company, Dordrecht, Holland, 1981. #Cordes2002 pmid=12417206 #Daura1999 X Daura, K Gademann, B Jaun, D Seebach, WF van Gunsteren, and AE Mark. ''Peptide folding: When simulation meets experiment''. Angewandte Chemie-International Edition, 38 (1-2):236–240, 1999. [http://dx.doi.org/10.1002/(SICI)1521-3773(19990115)38:1/2%3C236::AID-ANIE236%3E3.0.CO;2-M <nowiki>10.1002/(SICI)1521-3773(19990115)38:1/2<236::AID-ANIE236>3.0.CO;2-M</nowiki>]. </biblio> [[Category:Hippo]] [[Category:Software]] aa96a0f3171829b8f89faaca2931260c6b0122fc 114 112 2008-10-17T21:48:52Z Oliver 2 restructured installation wikitext text/x-wiki [[Image:Gbim.jpg‎|frame|right|A peptide folds and inserts into a membrane; the membrane is represented by an implicit Generalized Born model.]] '''Hippo''' is a software package for simulation and analysis of bio-molecules at an atomic level. It has been specifically developed for very efficient protein folding studies in aqueous and membrane environments. The code is very fast due to optimized and hand-coded assembly routines which make use of fast multi-media instructions on modern x86 cpus. Hippo is (partially) parallelized (using industry-standard [http://www.openmp.org/ openMP]). == Installation == === Download === Binaries are publicly available from the [http://www.biowerkzeug.com/ Biowerkzeg.com download page] for '''Linux''' and '''Windows'''. <!-- , and '''Mac OS X (Intel platform only)'''. --> === Installing the software === Unzip the downloaded file. It will unpack into its own <tt>hippo</tt> directory where you will find * compiled executables (see below) ** <tt>hippo</tt>: the MD and MC program ** <tt>analyse</tt>: the analysis program * the manual ([http://www.biowerkzeug.de/downloads/hippo/hippo_manual.pdf pdf]) * the [[Hippo license|license]] (to which you consent by downloading) * the OPLS-AA forcefield file (in Hippo format) * the readme.txt file * the <tt>testjobs</tt> directory with example systems The package includes binaries that run under Linux and Windows on any Intel or AMD processor that has the SSE or SSSE3 multi media instructions. Depending on your system and needs, choose the following executable from the package: {| |+Hippo executables !cpu !!Linux !!Windows |- |SSSE3 (Core Duo,...) ||<tt>hippo</tt> ||<tt>hippo.exe</tt> |- |SSE (PIII,P4,Athlon,...) ||<tt>hippo_p3</tt> ||<tt>hippo_p3.exe</tt> |} If in doubt, simply try them out in order; if it will not run you will receive an error message such as Fatal Error: This program was not built to run on the processor in your system. The allowed processors are: Intel(R) Core(TM) Duo processors and compatible Intel processors with supplemental Streaming SIMD Extensions 3 (SSSE3) instruction support. In this case try the <tt>hippo_p3</tt> or <tt>hippo_p3.exe</tt> executable. If this still doesn't work, [http://forums.biowerkzeug.org/viewforum.php?f=6 post a request in the Hippo Installation forum]. Executables with the <tt>_mpi</tt> extension have been compiled with OpenMP and can run on multiple CPUs. However, not all code segments are yet parallelized. === Test cases === The <tt>testjobs</tt> directory contains a number of testcases. Run the <tt>calc_testjobs_linux.bat</tt> or <tt>calc_testjobs_win32.bat</tt> script in order to perform ''all'' tests. On modern processors this should take between 2 and 4 Minutes. Use the tests in order to get started in running your own systems. == Features == === Simulation methods === * [[Molecular dynamics]] (MD) in NVT, NPT, NVE ensembles * Metropolis [[Monte Carlo]] (MC) in NVT and NPT ensembles <cite>JACS2004,JPhysChemB2006</cite> * [[Replica exchange]] with MD and MC === Force fields === * OPLS-AA <cite>Jorgensen1996,Kaminski2001</cite> === Solvation models === * explicit solvent (water: TIP4P <cite>Jorgensen1985</cite>, SPC <cite>Berendsen1981</cite>) * Generalized Born implicit solvent (GB/SA) * Generalized Born implicit membrane (GB/IM) <cite>Proteins2007,BJ2007,Proteins2005</cite> === Enhanced productivity === A number of features make it easy to use Hippo so that one can spend more time on working on problems and less time on setting up structures or dealing with system crashes: * seamless restarts * intelligent pdb structure loader: reads most pdbs, can complete missing atoms, and builds the topology * graphical frontend under development (Windows only) === Analysis === [[Image:Peptidescan.jpg|frame|right|Adiabatic Generalized Born energy surface for different positions and orientations of a helical peptide in a membrane (output from the ''translation+rotation energy scan'' analysis tool).]] A growing number of analysis tools are built into Hippo, for instance ; adiabatic translation+rotation energy scan: determines the Generalized Born energy of a peptide in a membrane <cite>MMB2008,BJ2006</cite>; this allows to decide if a (typically helical) peptide inserts into the membrane and at which depth and angle or if it prefers a surface-bound or even a fully solvated state ; RMSD: calculates the [[RMSD|root mean square deviation]] of trajectory frames to a reference structure ; helicity: degree of helicity of segments along trajectory ; Z - tilt - kink graph: Calculates center of mass, tilt angle, and kink angle of a peptide in a membrane as a function of simulation time. The membrane is in the xy plane, with z = 0 the membrane center. Kink angle is with respect to the membrane normal. <cite>Cordes2002</cite> ; cluster: Performs a cluster analysis using the pairwise method by Daura et al.<cite>Daura1999</cite> ; fit to phase: recenters trajectory on the centre of mass of a phase (such as a lipid membrane) ; fit solute to previous frames: Generate a PDB movie by RMSD fitting the solute of each frame to the previous frame. The Hippo output format is a binary [[File formats#xyz-movie|xyz-movie]] (see the [http://openbabel.org/wiki/XYZ definition of the xyz format]); thus many other [[analysis]] tools can also be used. == References == <biblio> #MMB2008 pmid=18428040 #Proteins2007 pmid=17600830 #BJ2007 pmid=17218457 #BJ2006 pmid=16339877 #JPhysChemB2006 pmid=16913813 #Proteins2005 pmid=15723347 #JACS2004 pmid=14871118 #Kaminski2001 George A. Kaminski, Richard A. Friesner, Julian Tirado-Rives, and William L. Jorgensen. ''Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides''. J. Phys. Chem. B, 105(28):6474–6487, 2001. [http://dx.doi.org/10.1021/jp003919d 10.1021/jp003919d]. #Jorgensen1996 W. L. Jorgensen, D. S. Maxwell, and J. Tirado-Rives. ''Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids''. J. Am. Chem. Soc., 118(45):11225–11236, 1996. [http://dx.doi.org/10.1021/ja9621760 10.1021/ja9621760]. #Jorgensen1985 W. L. Jorgensen and J. D. Madura. ''Temperature and size dependence for Monte-Carlo simulations of TIP4P water''. Mol. Phys., 56(6):1381–1392, December 1985. #Berendsen1981 H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, and J. Hermans. ''Interaction models for water in relation to protein hydration''. In B. Pullman, editor, Intermolecular Forces, page 331. D. Reidel Publishing Company, Dordrecht, Holland, 1981. #Cordes2002 pmid=12417206 #Daura1999 X Daura, K Gademann, B Jaun, D Seebach, WF van Gunsteren, and AE Mark. ''Peptide folding: When simulation meets experiment''. Angewandte Chemie-International Edition, 38 (1-2):236–240, 1999. [http://dx.doi.org/10.1002/(SICI)1521-3773(19990115)38:1/2%3C236::AID-ANIE236%3E3.0.CO;2-M <nowiki>10.1002/(SICI)1521-3773(19990115)38:1/2<236::AID-ANIE236>3.0.CO;2-M</nowiki>]. </biblio> [[Category:Hippo]] [[Category:Software]] 8fef1b36cf1dcba69f3656b2ed463907fa486eae 115 114 2008-10-17T21:50:10Z Oliver 2 put Features first wikitext text/x-wiki [[Image:Gbim.jpg‎|frame|right|A peptide folds and inserts into a membrane; the membrane is represented by an implicit Generalized Born model.]] '''Hippo''' is a software package for simulation and analysis of bio-molecules at an atomic level. It has been specifically developed for very efficient protein folding studies in aqueous and membrane environments. The code is very fast due to optimized and hand-coded assembly routines which make use of fast multi-media instructions on modern x86 cpus. Hippo is (partially) parallelized (using industry-standard [http://www.openmp.org/ openMP]). == Features == === Simulation methods === * [[Molecular dynamics]] (MD) in NVT, NPT, NVE ensembles * Metropolis [[Monte Carlo]] (MC) in NVT and NPT ensembles <cite>JACS2004,JPhysChemB2006</cite> * [[Replica exchange]] with MD and MC === Force fields === * OPLS-AA <cite>Jorgensen1996,Kaminski2001</cite> === Solvation models === * explicit solvent (water: TIP4P <cite>Jorgensen1985</cite>, SPC <cite>Berendsen1981</cite>) * Generalized Born implicit solvent (GB/SA) * Generalized Born implicit membrane (GB/IM) <cite>Proteins2007,BJ2007,Proteins2005</cite> === Enhanced productivity === A number of features make it easy to use Hippo so that one can spend more time on working on problems and less time on setting up structures or dealing with system crashes: * seamless restarts * intelligent pdb structure loader: reads most pdbs, can complete missing atoms, and builds the topology * graphical frontend under development (Windows only) === Analysis === [[Image:Peptidescan.jpg|frame|right|Adiabatic Generalized Born energy surface for different positions and orientations of a helical peptide in a membrane (output from the ''translation+rotation energy scan'' analysis tool).]] A growing number of analysis tools are built into Hippo, for instance ; adiabatic translation+rotation energy scan: determines the Generalized Born energy of a peptide in a membrane <cite>MMB2008,BJ2006</cite>; this allows to decide if a (typically helical) peptide inserts into the membrane and at which depth and angle or if it prefers a surface-bound or even a fully solvated state ; RMSD: calculates the [[RMSD|root mean square deviation]] of trajectory frames to a reference structure ; helicity: degree of helicity of segments along trajectory ; Z - tilt - kink graph: Calculates center of mass, tilt angle, and kink angle of a peptide in a membrane as a function of simulation time. The membrane is in the xy plane, with z = 0 the membrane center. Kink angle is with respect to the membrane normal. <cite>Cordes2002</cite> ; cluster: Performs a cluster analysis using the pairwise method by Daura et al.<cite>Daura1999</cite> ; fit to phase: recenters trajectory on the centre of mass of a phase (such as a lipid membrane) ; fit solute to previous frames: Generate a PDB movie by RMSD fitting the solute of each frame to the previous frame. The Hippo output format is a binary [[File formats#xyz-movie|xyz-movie]] (see the [http://openbabel.org/wiki/XYZ definition of the xyz format]); thus many other [[analysis]] tools can also be used. == Installation == === Download === Binaries are publicly available from the [http://www.biowerkzeug.com/ Biowerkzeg.com download page] for '''Linux''' and '''Windows'''. <!-- , and '''Mac OS X (Intel platform only)'''. --> === Installing the software === Unzip the downloaded file. It will unpack into its own <tt>hippo</tt> directory where you will find * compiled executables (see below) ** <tt>hippo</tt>: the MD and MC program ** <tt>analyse</tt>: the analysis program * the manual ([http://www.biowerkzeug.de/downloads/hippo/hippo_manual.pdf pdf]) * the [[Hippo license|license]] (to which you consent by downloading) * the OPLS-AA forcefield file (in Hippo format) * the readme.txt file * the <tt>testjobs</tt> directory with example systems The package includes binaries that run under Linux and Windows on any Intel or AMD processor that has the SSE or SSSE3 multi media instructions. Depending on your system and needs, choose the following executable from the package: {| |+Hippo executables !cpu !!Linux !!Windows |- |SSSE3 (Core Duo,...) ||<tt>hippo</tt> ||<tt>hippo.exe</tt> |- |SSE (PIII,P4,Athlon,...) ||<tt>hippo_p3</tt> ||<tt>hippo_p3.exe</tt> |} If in doubt, simply try them out in order; if it will not run you will receive an error message such as Fatal Error: This program was not built to run on the processor in your system. The allowed processors are: Intel(R) Core(TM) Duo processors and compatible Intel processors with supplemental Streaming SIMD Extensions 3 (SSSE3) instruction support. In this case try the <tt>hippo_p3</tt> or <tt>hippo_p3.exe</tt> executable. If this still doesn't work, [http://forums.biowerkzeug.org/viewforum.php?f=6 post a request in the Hippo Installation forum]. Executables with the <tt>_mpi</tt> extension have been compiled with OpenMP and can run on multiple CPUs. However, not all code segments are yet parallelized. === Test cases === The <tt>testjobs</tt> directory contains a number of testcases. Run the <tt>calc_testjobs_linux.bat</tt> or <tt>calc_testjobs_win32.bat</tt> script in order to perform ''all'' tests. On modern processors this should take between 2 and 4 Minutes. Use the tests in order to get started in running your own systems. == References == <biblio> #MMB2008 pmid=18428040 #Proteins2007 pmid=17600830 #BJ2007 pmid=17218457 #BJ2006 pmid=16339877 #JPhysChemB2006 pmid=16913813 #Proteins2005 pmid=15723347 #JACS2004 pmid=14871118 #Kaminski2001 George A. Kaminski, Richard A. Friesner, Julian Tirado-Rives, and William L. Jorgensen. ''Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides''. J. Phys. Chem. B, 105(28):6474–6487, 2001. [http://dx.doi.org/10.1021/jp003919d 10.1021/jp003919d]. #Jorgensen1996 W. L. Jorgensen, D. S. Maxwell, and J. Tirado-Rives. ''Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids''. J. Am. Chem. Soc., 118(45):11225–11236, 1996. [http://dx.doi.org/10.1021/ja9621760 10.1021/ja9621760]. #Jorgensen1985 W. L. Jorgensen and J. D. Madura. ''Temperature and size dependence for Monte-Carlo simulations of TIP4P water''. Mol. Phys., 56(6):1381–1392, December 1985. #Berendsen1981 H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, and J. Hermans. ''Interaction models for water in relation to protein hydration''. In B. Pullman, editor, Intermolecular Forces, page 331. D. Reidel Publishing Company, Dordrecht, Holland, 1981. #Cordes2002 pmid=12417206 #Daura1999 X Daura, K Gademann, B Jaun, D Seebach, WF van Gunsteren, and AE Mark. ''Peptide folding: When simulation meets experiment''. Angewandte Chemie-International Edition, 38 (1-2):236–240, 1999. [http://dx.doi.org/10.1002/(SICI)1521-3773(19990115)38:1/2%3C236::AID-ANIE236%3E3.0.CO;2-M <nowiki>10.1002/(SICI)1521-3773(19990115)38:1/2<236::AID-ANIE236>3.0.CO;2-M</nowiki>]. </biblio> [[Category:Hippo]] [[Category:Software]] d2a115d097a68f19dfe016795c203fa6b8f747df 116 115 2008-10-17T21:50:38Z Oliver 2 wikitext text/x-wiki [[Image:Gbim.jpg‎|frame|right|A peptide folds and inserts into a membrane; the membrane is represented by an implicit Generalized Born model.]] '''Hippo''' is a software package for simulation and analysis of bio-molecules at an atomic level. It has been specifically developed for very efficient protein folding studies in aqueous and membrane environments. The code is very fast due to optimized and hand-coded assembly routines which make use of fast multi-media instructions on modern x86 cpus. Hippo is (partially) parallelized (using industry-standard [http://www.openmp.org/ OpenMP]). == Features == === Simulation methods === * [[Molecular dynamics]] (MD) in NVT, NPT, NVE ensembles * Metropolis [[Monte Carlo]] (MC) in NVT and NPT ensembles <cite>JACS2004,JPhysChemB2006</cite> * [[Replica exchange]] with MD and MC === Force fields === * OPLS-AA <cite>Jorgensen1996,Kaminski2001</cite> === Solvation models === * explicit solvent (water: TIP4P <cite>Jorgensen1985</cite>, SPC <cite>Berendsen1981</cite>) * Generalized Born implicit solvent (GB/SA) * Generalized Born implicit membrane (GB/IM) <cite>Proteins2007,BJ2007,Proteins2005</cite> === Enhanced productivity === A number of features make it easy to use Hippo so that one can spend more time on working on problems and less time on setting up structures or dealing with system crashes: * seamless restarts * intelligent pdb structure loader: reads most pdbs, can complete missing atoms, and builds the topology * graphical frontend under development (Windows only) === Analysis === [[Image:Peptidescan.jpg|frame|right|Adiabatic Generalized Born energy surface for different positions and orientations of a helical peptide in a membrane (output from the ''translation+rotation energy scan'' analysis tool).]] A growing number of analysis tools are built into Hippo, for instance ; adiabatic translation+rotation energy scan: determines the Generalized Born energy of a peptide in a membrane <cite>MMB2008,BJ2006</cite>; this allows to decide if a (typically helical) peptide inserts into the membrane and at which depth and angle or if it prefers a surface-bound or even a fully solvated state ; RMSD: calculates the [[RMSD|root mean square deviation]] of trajectory frames to a reference structure ; helicity: degree of helicity of segments along trajectory ; Z - tilt - kink graph: Calculates center of mass, tilt angle, and kink angle of a peptide in a membrane as a function of simulation time. The membrane is in the xy plane, with z = 0 the membrane center. Kink angle is with respect to the membrane normal. <cite>Cordes2002</cite> ; cluster: Performs a cluster analysis using the pairwise method by Daura et al.<cite>Daura1999</cite> ; fit to phase: recenters trajectory on the centre of mass of a phase (such as a lipid membrane) ; fit solute to previous frames: Generate a PDB movie by RMSD fitting the solute of each frame to the previous frame. The Hippo output format is a binary [[File formats#xyz-movie|xyz-movie]] (see the [http://openbabel.org/wiki/XYZ definition of the xyz format]); thus many other [[analysis]] tools can also be used. == Installation == === Download === Binaries are publicly available from the [http://www.biowerkzeug.com/ Biowerkzeg.com download page] for '''Linux''' and '''Windows'''. <!-- , and '''Mac OS X (Intel platform only)'''. --> === Installing the software === Unzip the downloaded file. It will unpack into its own <tt>hippo</tt> directory where you will find * compiled executables (see below) ** <tt>hippo</tt>: the MD and MC program ** <tt>analyse</tt>: the analysis program * the manual ([http://www.biowerkzeug.de/downloads/hippo/hippo_manual.pdf pdf]) * the [[Hippo license|license]] (to which you consent by downloading) * the OPLS-AA forcefield file (in Hippo format) * the readme.txt file * the <tt>testjobs</tt> directory with example systems The package includes binaries that run under Linux and Windows on any Intel or AMD processor that has the SSE or SSSE3 multi media instructions. Depending on your system and needs, choose the following executable from the package: {| |+Hippo executables !cpu !!Linux !!Windows |- |SSSE3 (Core Duo,...) ||<tt>hippo</tt> ||<tt>hippo.exe</tt> |- |SSE (PIII,P4,Athlon,...) ||<tt>hippo_p3</tt> ||<tt>hippo_p3.exe</tt> |} If in doubt, simply try them out in order; if it will not run you will receive an error message such as Fatal Error: This program was not built to run on the processor in your system. The allowed processors are: Intel(R) Core(TM) Duo processors and compatible Intel processors with supplemental Streaming SIMD Extensions 3 (SSSE3) instruction support. In this case try the <tt>hippo_p3</tt> or <tt>hippo_p3.exe</tt> executable. If this still doesn't work, [http://forums.biowerkzeug.org/viewforum.php?f=6 post a request in the Hippo Installation forum]. Executables with the <tt>_mpi</tt> extension have been compiled with OpenMP and can run on multiple CPUs. However, not all code segments are yet parallelized. === Test cases === The <tt>testjobs</tt> directory contains a number of testcases. Run the <tt>calc_testjobs_linux.bat</tt> or <tt>calc_testjobs_win32.bat</tt> script in order to perform ''all'' tests. On modern processors this should take between 2 and 4 Minutes. Use the tests in order to get started in running your own systems. == References == <biblio> #MMB2008 pmid=18428040 #Proteins2007 pmid=17600830 #BJ2007 pmid=17218457 #BJ2006 pmid=16339877 #JPhysChemB2006 pmid=16913813 #Proteins2005 pmid=15723347 #JACS2004 pmid=14871118 #Kaminski2001 George A. Kaminski, Richard A. Friesner, Julian Tirado-Rives, and William L. Jorgensen. ''Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides''. J. Phys. Chem. B, 105(28):6474–6487, 2001. [http://dx.doi.org/10.1021/jp003919d 10.1021/jp003919d]. #Jorgensen1996 W. L. Jorgensen, D. S. Maxwell, and J. Tirado-Rives. ''Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids''. J. Am. Chem. Soc., 118(45):11225–11236, 1996. [http://dx.doi.org/10.1021/ja9621760 10.1021/ja9621760]. #Jorgensen1985 W. L. Jorgensen and J. D. Madura. ''Temperature and size dependence for Monte-Carlo simulations of TIP4P water''. Mol. Phys., 56(6):1381–1392, December 1985. #Berendsen1981 H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, and J. Hermans. ''Interaction models for water in relation to protein hydration''. In B. Pullman, editor, Intermolecular Forces, page 331. D. Reidel Publishing Company, Dordrecht, Holland, 1981. #Cordes2002 pmid=12417206 #Daura1999 X Daura, K Gademann, B Jaun, D Seebach, WF van Gunsteren, and AE Mark. ''Peptide folding: When simulation meets experiment''. Angewandte Chemie-International Edition, 38 (1-2):236–240, 1999. [http://dx.doi.org/10.1002/(SICI)1521-3773(19990115)38:1/2%3C236::AID-ANIE236%3E3.0.CO;2-M <nowiki>10.1002/(SICI)1521-3773(19990115)38:1/2<236::AID-ANIE236>3.0.CO;2-M</nowiki>]. </biblio> [[Category:Hippo]] [[Category:Software]] 80458a86417b94978428fa50635b4839768f5c65 118 116 2008-10-17T22:05:00Z Oliver 2 /* Installing the software */ wikitext text/x-wiki [[Image:Gbim.jpg‎|frame|right|A peptide folds and inserts into a membrane; the membrane is represented by an implicit Generalized Born model.]] '''Hippo''' is a software package for simulation and analysis of bio-molecules at an atomic level. It has been specifically developed for very efficient protein folding studies in aqueous and membrane environments. The code is very fast due to optimized and hand-coded assembly routines which make use of fast multi-media instructions on modern x86 cpus. Hippo is (partially) parallelized (using industry-standard [http://www.openmp.org/ OpenMP]). == Features == === Simulation methods === * [[Molecular dynamics]] (MD) in NVT, NPT, NVE ensembles * Metropolis [[Monte Carlo]] (MC) in NVT and NPT ensembles <cite>JACS2004,JPhysChemB2006</cite> * [[Replica exchange]] with MD and MC === Force fields === * OPLS-AA <cite>Jorgensen1996,Kaminski2001</cite> === Solvation models === * explicit solvent (water: TIP4P <cite>Jorgensen1985</cite>, SPC <cite>Berendsen1981</cite>) * Generalized Born implicit solvent (GB/SA) * Generalized Born implicit membrane (GB/IM) <cite>Proteins2007,BJ2007,Proteins2005</cite> === Enhanced productivity === A number of features make it easy to use Hippo so that one can spend more time on working on problems and less time on setting up structures or dealing with system crashes: * seamless restarts * intelligent pdb structure loader: reads most pdbs, can complete missing atoms, and builds the topology * graphical frontend under development (Windows only) === Analysis === [[Image:Peptidescan.jpg|frame|right|Adiabatic Generalized Born energy surface for different positions and orientations of a helical peptide in a membrane (output from the ''translation+rotation energy scan'' analysis tool).]] A growing number of analysis tools are built into Hippo, for instance ; adiabatic translation+rotation energy scan: determines the Generalized Born energy of a peptide in a membrane <cite>MMB2008,BJ2006</cite>; this allows to decide if a (typically helical) peptide inserts into the membrane and at which depth and angle or if it prefers a surface-bound or even a fully solvated state ; RMSD: calculates the [[RMSD|root mean square deviation]] of trajectory frames to a reference structure ; helicity: degree of helicity of segments along trajectory ; Z - tilt - kink graph: Calculates center of mass, tilt angle, and kink angle of a peptide in a membrane as a function of simulation time. The membrane is in the xy plane, with z = 0 the membrane center. Kink angle is with respect to the membrane normal. <cite>Cordes2002</cite> ; cluster: Performs a cluster analysis using the pairwise method by Daura et al.<cite>Daura1999</cite> ; fit to phase: recenters trajectory on the centre of mass of a phase (such as a lipid membrane) ; fit solute to previous frames: Generate a PDB movie by RMSD fitting the solute of each frame to the previous frame. The Hippo output format is a binary [[File formats#xyz-movie|xyz-movie]] (see the [http://openbabel.org/wiki/XYZ definition of the xyz format]); thus many other [[analysis]] tools can also be used. == Installation == === Download === Binaries are publicly available from the [http://www.biowerkzeug.com/ Biowerkzeg.com download page] for '''Linux''' and '''Windows'''. <!-- , and '''Mac OS X (Intel platform only)'''. --> === Installing the software === Unzip the downloaded file. It will unpack into its own <tt>hippo</tt> directory where you will find * compiled executables (see below) ** <tt>hippo</tt>: the MD and MC program ** <tt>analyse</tt>: the analysis program * the manual ([http://www.biowerkzeug.de/downloads/hippo/hippo_manual.pdf pdf]) * the [[Hippo license|license]] (to which you consent by downloading) * the OPLS-AA forcefield file (in Hippo format) * the readme.txt file * the <tt>testjobs</tt> directory with example systems The package includes binaries that run under Linux and Windows on any Intel or AMD processor that has the SSE or SSSE3 multi media instructions. Depending on your system and needs, choose the an executable from the package as shown in the table: {| class="wikitable" |+Hippo executables !cpu !!Linux !!Windows |- |SSSE3 (Core Duo,...) ||<tt>hippo</tt> ||<tt>hippo.exe</tt> |- |SSE (PIII,P4,Athlon,...) ||<tt>hippo_p3</tt> ||<tt>hippo_p3.exe</tt> |} If in doubt, simply try them out in order; if it will not run you will receive an error message such as Fatal Error: This program was not built to run on the processor in your system. The allowed processors are: Intel(R) Core(TM) Duo processors and compatible Intel processors with supplemental Streaming SIMD Extensions 3 (SSSE3) instruction support. In this case try the <tt>hippo_p3</tt> or <tt>hippo_p3.exe</tt> executable. If this still doesn't work, [http://forums.biowerkzeug.org/viewforum.php?f=6 post a request in the Hippo Installation forum]. Executables with the <tt>_mpi</tt> extension have been compiled with OpenMP and can run on multiple CPUs. However, not all code segments are yet parallelized. === Test cases === The <tt>testjobs</tt> directory contains a number of testcases. Run the <tt>calc_testjobs_linux.bat</tt> or <tt>calc_testjobs_win32.bat</tt> script in order to perform ''all'' tests. On modern processors this should take between 2 and 4 Minutes. Use the tests in order to get started in running your own systems. == References == <biblio> #MMB2008 pmid=18428040 #Proteins2007 pmid=17600830 #BJ2007 pmid=17218457 #BJ2006 pmid=16339877 #JPhysChemB2006 pmid=16913813 #Proteins2005 pmid=15723347 #JACS2004 pmid=14871118 #Kaminski2001 George A. Kaminski, Richard A. Friesner, Julian Tirado-Rives, and William L. Jorgensen. ''Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides''. J. Phys. Chem. B, 105(28):6474–6487, 2001. [http://dx.doi.org/10.1021/jp003919d 10.1021/jp003919d]. #Jorgensen1996 W. L. Jorgensen, D. S. Maxwell, and J. Tirado-Rives. ''Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids''. J. Am. Chem. Soc., 118(45):11225–11236, 1996. [http://dx.doi.org/10.1021/ja9621760 10.1021/ja9621760]. #Jorgensen1985 W. L. Jorgensen and J. D. Madura. ''Temperature and size dependence for Monte-Carlo simulations of TIP4P water''. Mol. Phys., 56(6):1381–1392, December 1985. #Berendsen1981 H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, and J. Hermans. ''Interaction models for water in relation to protein hydration''. In B. Pullman, editor, Intermolecular Forces, page 331. D. Reidel Publishing Company, Dordrecht, Holland, 1981. #Cordes2002 pmid=12417206 #Daura1999 X Daura, K Gademann, B Jaun, D Seebach, WF van Gunsteren, and AE Mark. ''Peptide folding: When simulation meets experiment''. Angewandte Chemie-International Edition, 38 (1-2):236–240, 1999. [http://dx.doi.org/10.1002/(SICI)1521-3773(19990115)38:1/2%3C236::AID-ANIE236%3E3.0.CO;2-M <nowiki>10.1002/(SICI)1521-3773(19990115)38:1/2<236::AID-ANIE236>3.0.CO;2-M</nowiki>]. </biblio> [[Category:Hippo]] [[Category:Software]] 87cd2713ea879005855b4955ff824f6f38fd4aab 119 118 2008-10-17T22:06:54Z Oliver 2 /* Installing the software */ floating table wikitext text/x-wiki [[Image:Gbim.jpg‎|frame|right|A peptide folds and inserts into a membrane; the membrane is represented by an implicit Generalized Born model.]] '''Hippo''' is a software package for simulation and analysis of bio-molecules at an atomic level. It has been specifically developed for very efficient protein folding studies in aqueous and membrane environments. The code is very fast due to optimized and hand-coded assembly routines which make use of fast multi-media instructions on modern x86 cpus. Hippo is (partially) parallelized (using industry-standard [http://www.openmp.org/ OpenMP]). == Features == === Simulation methods === * [[Molecular dynamics]] (MD) in NVT, NPT, NVE ensembles * Metropolis [[Monte Carlo]] (MC) in NVT and NPT ensembles <cite>JACS2004,JPhysChemB2006</cite> * [[Replica exchange]] with MD and MC === Force fields === * OPLS-AA <cite>Jorgensen1996,Kaminski2001</cite> === Solvation models === * explicit solvent (water: TIP4P <cite>Jorgensen1985</cite>, SPC <cite>Berendsen1981</cite>) * Generalized Born implicit solvent (GB/SA) * Generalized Born implicit membrane (GB/IM) <cite>Proteins2007,BJ2007,Proteins2005</cite> === Enhanced productivity === A number of features make it easy to use Hippo so that one can spend more time on working on problems and less time on setting up structures or dealing with system crashes: * seamless restarts * intelligent pdb structure loader: reads most pdbs, can complete missing atoms, and builds the topology * graphical frontend under development (Windows only) === Analysis === [[Image:Peptidescan.jpg|frame|right|Adiabatic Generalized Born energy surface for different positions and orientations of a helical peptide in a membrane (output from the ''translation+rotation energy scan'' analysis tool).]] A growing number of analysis tools are built into Hippo, for instance ; adiabatic translation+rotation energy scan: determines the Generalized Born energy of a peptide in a membrane <cite>MMB2008,BJ2006</cite>; this allows to decide if a (typically helical) peptide inserts into the membrane and at which depth and angle or if it prefers a surface-bound or even a fully solvated state ; RMSD: calculates the [[RMSD|root mean square deviation]] of trajectory frames to a reference structure ; helicity: degree of helicity of segments along trajectory ; Z - tilt - kink graph: Calculates center of mass, tilt angle, and kink angle of a peptide in a membrane as a function of simulation time. The membrane is in the xy plane, with z = 0 the membrane center. Kink angle is with respect to the membrane normal. <cite>Cordes2002</cite> ; cluster: Performs a cluster analysis using the pairwise method by Daura et al.<cite>Daura1999</cite> ; fit to phase: recenters trajectory on the centre of mass of a phase (such as a lipid membrane) ; fit solute to previous frames: Generate a PDB movie by RMSD fitting the solute of each frame to the previous frame. The Hippo output format is a binary [[File formats#xyz-movie|xyz-movie]] (see the [http://openbabel.org/wiki/XYZ definition of the xyz format]); thus many other [[analysis]] tools can also be used. == Installation == === Download === Binaries are publicly available from the [http://www.biowerkzeug.com/ Biowerkzeg.com download page] for '''Linux''' and '''Windows'''. <!-- , and '''Mac OS X (Intel platform only)'''. --> === Installing the software === Unzip the downloaded file. It will unpack into its own <tt>hippo</tt> directory where you will find * compiled executables (see below) ** <tt>hippo</tt>: the MD and MC program ** <tt>analyse</tt>: the analysis program * the manual ([http://www.biowerkzeug.de/downloads/hippo/hippo_manual.pdf pdf]) * the [[Hippo license|license]] (to which you consent by downloading) * the OPLS-AA forcefield file (in Hippo format) * the readme.txt file * the <tt>testjobs</tt> directory with example systems {| class="wikitable" align="right" |+Hippo executables !cpu !!Linux !!Windows |- |SSSE3 (Core Duo,...) ||<tt>hippo</tt> ||<tt>hippo.exe</tt> |- |SSE (PIII,P4,Athlon,...) ||<tt>hippo_p3</tt> ||<tt>hippo_p3.exe</tt> |} The package includes binaries that run under Linux and Windows on any Intel or AMD processor that has the SSE or SSSE3 multi media instructions. Depending on your system and needs, choose an executable from the package as shown in the table ''Hippo executables''. If in doubt, simply try them out in order; if it will not run you will receive an error message such as Fatal Error: This program was not built to run on the processor in your system. The allowed processors are: Intel(R) Core(TM) Duo processors and compatible Intel processors with supplemental Streaming SIMD Extensions 3 (SSSE3) instruction support. In this case try the <tt>hippo_p3</tt> or <tt>hippo_p3.exe</tt> executable. If this still doesn't work, [http://forums.biowerkzeug.org/viewforum.php?f=6 post a request in the Hippo Installation forum]. Executables with the <tt>_mpi</tt> extension have been compiled with OpenMP and can run on multiple CPUs. However, not all code segments are yet parallelized. === Test cases === The <tt>testjobs</tt> directory contains a number of testcases. Run the <tt>calc_testjobs_linux.bat</tt> or <tt>calc_testjobs_win32.bat</tt> script in order to perform ''all'' tests. On modern processors this should take between 2 and 4 Minutes. Use the tests in order to get started in running your own systems. == References == <biblio> #MMB2008 pmid=18428040 #Proteins2007 pmid=17600830 #BJ2007 pmid=17218457 #BJ2006 pmid=16339877 #JPhysChemB2006 pmid=16913813 #Proteins2005 pmid=15723347 #JACS2004 pmid=14871118 #Kaminski2001 George A. Kaminski, Richard A. Friesner, Julian Tirado-Rives, and William L. Jorgensen. ''Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides''. J. Phys. Chem. B, 105(28):6474–6487, 2001. [http://dx.doi.org/10.1021/jp003919d 10.1021/jp003919d]. #Jorgensen1996 W. L. Jorgensen, D. S. Maxwell, and J. Tirado-Rives. ''Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids''. J. Am. Chem. Soc., 118(45):11225–11236, 1996. [http://dx.doi.org/10.1021/ja9621760 10.1021/ja9621760]. #Jorgensen1985 W. L. Jorgensen and J. D. Madura. ''Temperature and size dependence for Monte-Carlo simulations of TIP4P water''. Mol. Phys., 56(6):1381–1392, December 1985. #Berendsen1981 H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, and J. Hermans. ''Interaction models for water in relation to protein hydration''. In B. Pullman, editor, Intermolecular Forces, page 331. D. Reidel Publishing Company, Dordrecht, Holland, 1981. #Cordes2002 pmid=12417206 #Daura1999 X Daura, K Gademann, B Jaun, D Seebach, WF van Gunsteren, and AE Mark. ''Peptide folding: When simulation meets experiment''. Angewandte Chemie-International Edition, 38 (1-2):236–240, 1999. [http://dx.doi.org/10.1002/(SICI)1521-3773(19990115)38:1/2%3C236::AID-ANIE236%3E3.0.CO;2-M <nowiki>10.1002/(SICI)1521-3773(19990115)38:1/2<236::AID-ANIE236>3.0.CO;2-M</nowiki>]. </biblio> [[Category:Hippo]] [[Category:Software]] 3e7e4295a505bb6823eb75d3b4a622e9e6c8d53a 120 119 2008-10-17T22:08:39Z Oliver 2 /* Installing the software */ links wikitext text/x-wiki [[Image:Gbim.jpg‎|frame|right|A peptide folds and inserts into a membrane; the membrane is represented by an implicit Generalized Born model.]] '''Hippo''' is a software package for simulation and analysis of bio-molecules at an atomic level. It has been specifically developed for very efficient protein folding studies in aqueous and membrane environments. The code is very fast due to optimized and hand-coded assembly routines which make use of fast multi-media instructions on modern x86 cpus. Hippo is (partially) parallelized (using industry-standard [http://www.openmp.org/ OpenMP]). == Features == === Simulation methods === * [[Molecular dynamics]] (MD) in NVT, NPT, NVE ensembles * Metropolis [[Monte Carlo]] (MC) in NVT and NPT ensembles <cite>JACS2004,JPhysChemB2006</cite> * [[Replica exchange]] with MD and MC === Force fields === * OPLS-AA <cite>Jorgensen1996,Kaminski2001</cite> === Solvation models === * explicit solvent (water: TIP4P <cite>Jorgensen1985</cite>, SPC <cite>Berendsen1981</cite>) * Generalized Born implicit solvent (GB/SA) * Generalized Born implicit membrane (GB/IM) <cite>Proteins2007,BJ2007,Proteins2005</cite> === Enhanced productivity === A number of features make it easy to use Hippo so that one can spend more time on working on problems and less time on setting up structures or dealing with system crashes: * seamless restarts * intelligent pdb structure loader: reads most pdbs, can complete missing atoms, and builds the topology * graphical frontend under development (Windows only) === Analysis === [[Image:Peptidescan.jpg|frame|right|Adiabatic Generalized Born energy surface for different positions and orientations of a helical peptide in a membrane (output from the ''translation+rotation energy scan'' analysis tool).]] A growing number of analysis tools are built into Hippo, for instance ; adiabatic translation+rotation energy scan: determines the Generalized Born energy of a peptide in a membrane <cite>MMB2008,BJ2006</cite>; this allows to decide if a (typically helical) peptide inserts into the membrane and at which depth and angle or if it prefers a surface-bound or even a fully solvated state ; RMSD: calculates the [[RMSD|root mean square deviation]] of trajectory frames to a reference structure ; helicity: degree of helicity of segments along trajectory ; Z - tilt - kink graph: Calculates center of mass, tilt angle, and kink angle of a peptide in a membrane as a function of simulation time. The membrane is in the xy plane, with z = 0 the membrane center. Kink angle is with respect to the membrane normal. <cite>Cordes2002</cite> ; cluster: Performs a cluster analysis using the pairwise method by Daura et al.<cite>Daura1999</cite> ; fit to phase: recenters trajectory on the centre of mass of a phase (such as a lipid membrane) ; fit solute to previous frames: Generate a PDB movie by RMSD fitting the solute of each frame to the previous frame. The Hippo output format is a binary [[File formats#xyz-movie|xyz-movie]] (see the [http://openbabel.org/wiki/XYZ definition of the xyz format]); thus many other [[analysis]] tools can also be used. == Installation == === Download === Binaries are publicly available from the [http://www.biowerkzeug.com/ Biowerkzeg.com download page] for '''Linux''' and '''Windows'''. <!-- , and '''Mac OS X (Intel platform only)'''. --> === Installing the software === Unzip the downloaded file. It will unpack into its own <tt>hippo</tt> directory where you will find * compiled executables (see below) ** <tt>hippo</tt>: the [[#Simulation methods|MD and MC program]] ** <tt>analyse</tt>: the[[#Analysis|analysis program]] * the manual ([http://www.biowerkzeug.de/downloads/hippo/hippo_manual.pdf pdf]) * the [[Hippo license|license]] (to which you consent by downloading) * the OPLS-AA forcefield file (in Hippo format) * the readme.txt file * the <tt>testjobs</tt> directory with example systems {| class="wikitable" align="right" |+Hippo executables !cpu !!Linux !!Windows |- |SSSE3 (Core Duo,...) ||<tt>hippo</tt> ||<tt>hippo.exe</tt> |- |SSE (PIII,P4,Athlon,...) ||<tt>hippo_p3</tt> ||<tt>hippo_p3.exe</tt> |} The package includes binaries that run under Linux and Windows on any Intel or AMD processor that has the SSE or SSSE3 multi media instructions. Depending on your system and needs, choose an executable from the package as shown in the table ''Hippo executables''. If in doubt, simply try them out in order; if it will not run you will receive an error message such as Fatal Error: This program was not built to run on the processor in your system. The allowed processors are: Intel(R) Core(TM) Duo processors and compatible Intel processors with supplemental Streaming SIMD Extensions 3 (SSSE3) instruction support. In this case try the <tt>hippo_p3</tt> or <tt>hippo_p3.exe</tt> executable. If this still doesn't work, [http://forums.biowerkzeug.org/viewforum.php?f=6 post a request in the Hippo Installation forum]. Executables with the <tt>_mpi</tt> extension have been compiled with OpenMP and can run on multiple CPUs. However, not all code segments are yet parallelized. === Test cases === The <tt>testjobs</tt> directory contains a number of testcases. Run the <tt>calc_testjobs_linux.bat</tt> or <tt>calc_testjobs_win32.bat</tt> script in order to perform ''all'' tests. On modern processors this should take between 2 and 4 Minutes. Use the tests in order to get started in running your own systems. == References == <biblio> #MMB2008 pmid=18428040 #Proteins2007 pmid=17600830 #BJ2007 pmid=17218457 #BJ2006 pmid=16339877 #JPhysChemB2006 pmid=16913813 #Proteins2005 pmid=15723347 #JACS2004 pmid=14871118 #Kaminski2001 George A. Kaminski, Richard A. Friesner, Julian Tirado-Rives, and William L. Jorgensen. ''Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides''. J. Phys. Chem. B, 105(28):6474–6487, 2001. [http://dx.doi.org/10.1021/jp003919d 10.1021/jp003919d]. #Jorgensen1996 W. L. Jorgensen, D. S. Maxwell, and J. Tirado-Rives. ''Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids''. J. Am. Chem. Soc., 118(45):11225–11236, 1996. [http://dx.doi.org/10.1021/ja9621760 10.1021/ja9621760]. #Jorgensen1985 W. L. Jorgensen and J. D. Madura. ''Temperature and size dependence for Monte-Carlo simulations of TIP4P water''. Mol. Phys., 56(6):1381–1392, December 1985. #Berendsen1981 H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, and J. Hermans. ''Interaction models for water in relation to protein hydration''. In B. Pullman, editor, Intermolecular Forces, page 331. D. Reidel Publishing Company, Dordrecht, Holland, 1981. #Cordes2002 pmid=12417206 #Daura1999 X Daura, K Gademann, B Jaun, D Seebach, WF van Gunsteren, and AE Mark. ''Peptide folding: When simulation meets experiment''. Angewandte Chemie-International Edition, 38 (1-2):236–240, 1999. [http://dx.doi.org/10.1002/(SICI)1521-3773(19990115)38:1/2%3C236::AID-ANIE236%3E3.0.CO;2-M <nowiki>10.1002/(SICI)1521-3773(19990115)38:1/2<236::AID-ANIE236>3.0.CO;2-M</nowiki>]. </biblio> [[Category:Hippo]] [[Category:Software]] 12bd2d8f710cf98d4992caac861531ac216ddf1c 121 120 2008-10-17T22:09:02Z Oliver 2 /* Installing the software */ wikitext text/x-wiki [[Image:Gbim.jpg‎|frame|right|A peptide folds and inserts into a membrane; the membrane is represented by an implicit Generalized Born model.]] '''Hippo''' is a software package for simulation and analysis of bio-molecules at an atomic level. It has been specifically developed for very efficient protein folding studies in aqueous and membrane environments. The code is very fast due to optimized and hand-coded assembly routines which make use of fast multi-media instructions on modern x86 cpus. Hippo is (partially) parallelized (using industry-standard [http://www.openmp.org/ OpenMP]). == Features == === Simulation methods === * [[Molecular dynamics]] (MD) in NVT, NPT, NVE ensembles * Metropolis [[Monte Carlo]] (MC) in NVT and NPT ensembles <cite>JACS2004,JPhysChemB2006</cite> * [[Replica exchange]] with MD and MC === Force fields === * OPLS-AA <cite>Jorgensen1996,Kaminski2001</cite> === Solvation models === * explicit solvent (water: TIP4P <cite>Jorgensen1985</cite>, SPC <cite>Berendsen1981</cite>) * Generalized Born implicit solvent (GB/SA) * Generalized Born implicit membrane (GB/IM) <cite>Proteins2007,BJ2007,Proteins2005</cite> === Enhanced productivity === A number of features make it easy to use Hippo so that one can spend more time on working on problems and less time on setting up structures or dealing with system crashes: * seamless restarts * intelligent pdb structure loader: reads most pdbs, can complete missing atoms, and builds the topology * graphical frontend under development (Windows only) === Analysis === [[Image:Peptidescan.jpg|frame|right|Adiabatic Generalized Born energy surface for different positions and orientations of a helical peptide in a membrane (output from the ''translation+rotation energy scan'' analysis tool).]] A growing number of analysis tools are built into Hippo, for instance ; adiabatic translation+rotation energy scan: determines the Generalized Born energy of a peptide in a membrane <cite>MMB2008,BJ2006</cite>; this allows to decide if a (typically helical) peptide inserts into the membrane and at which depth and angle or if it prefers a surface-bound or even a fully solvated state ; RMSD: calculates the [[RMSD|root mean square deviation]] of trajectory frames to a reference structure ; helicity: degree of helicity of segments along trajectory ; Z - tilt - kink graph: Calculates center of mass, tilt angle, and kink angle of a peptide in a membrane as a function of simulation time. The membrane is in the xy plane, with z = 0 the membrane center. Kink angle is with respect to the membrane normal. <cite>Cordes2002</cite> ; cluster: Performs a cluster analysis using the pairwise method by Daura et al.<cite>Daura1999</cite> ; fit to phase: recenters trajectory on the centre of mass of a phase (such as a lipid membrane) ; fit solute to previous frames: Generate a PDB movie by RMSD fitting the solute of each frame to the previous frame. The Hippo output format is a binary [[File formats#xyz-movie|xyz-movie]] (see the [http://openbabel.org/wiki/XYZ definition of the xyz format]); thus many other [[analysis]] tools can also be used. == Installation == === Download === Binaries are publicly available from the [http://www.biowerkzeug.com/ Biowerkzeg.com download page] for '''Linux''' and '''Windows'''. <!-- , and '''Mac OS X (Intel platform only)'''. --> === Installing the software === Unzip the downloaded file. It will unpack into its own <tt>hippo</tt> directory where you will find * compiled executables (see below) ** <tt>hippo</tt>: the [[#Simulation methods|MD and MC program]] ** <tt>analyse</tt>: the [[#Analysis|analysis program]] * the manual ([http://www.biowerkzeug.de/downloads/hippo/hippo_manual.pdf pdf]) * the [[Hippo license|license]] (to which you consent by downloading) * the OPLS-AA forcefield file (in Hippo format) * the readme.txt file * the <tt>testjobs</tt> directory with example systems {| class="wikitable" align="right" |+Hippo executables !cpu !!Linux !!Windows |- |SSSE3 (Core Duo,...) ||<tt>hippo</tt> ||<tt>hippo.exe</tt> |- |SSE (PIII,P4,Athlon,...) ||<tt>hippo_p3</tt> ||<tt>hippo_p3.exe</tt> |} The package includes binaries that run under Linux and Windows on any Intel or AMD processor that has the SSE or SSSE3 multi media instructions. Depending on your system and needs, choose an executable from the package as shown in the table ''Hippo executables''. If in doubt, simply try them out in order; if it will not run you will receive an error message such as Fatal Error: This program was not built to run on the processor in your system. The allowed processors are: Intel(R) Core(TM) Duo processors and compatible Intel processors with supplemental Streaming SIMD Extensions 3 (SSSE3) instruction support. In this case try the <tt>hippo_p3</tt> or <tt>hippo_p3.exe</tt> executable. If this still doesn't work, [http://forums.biowerkzeug.org/viewforum.php?f=6 post a request in the Hippo Installation forum]. Executables with the <tt>_mpi</tt> extension have been compiled with OpenMP and can run on multiple CPUs. However, not all code segments are yet parallelized. === Test cases === The <tt>testjobs</tt> directory contains a number of testcases. Run the <tt>calc_testjobs_linux.bat</tt> or <tt>calc_testjobs_win32.bat</tt> script in order to perform ''all'' tests. On modern processors this should take between 2 and 4 Minutes. Use the tests in order to get started in running your own systems. == References == <biblio> #MMB2008 pmid=18428040 #Proteins2007 pmid=17600830 #BJ2007 pmid=17218457 #BJ2006 pmid=16339877 #JPhysChemB2006 pmid=16913813 #Proteins2005 pmid=15723347 #JACS2004 pmid=14871118 #Kaminski2001 George A. Kaminski, Richard A. Friesner, Julian Tirado-Rives, and William L. Jorgensen. ''Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides''. J. Phys. Chem. B, 105(28):6474–6487, 2001. [http://dx.doi.org/10.1021/jp003919d 10.1021/jp003919d]. #Jorgensen1996 W. L. Jorgensen, D. S. Maxwell, and J. Tirado-Rives. ''Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids''. J. Am. Chem. Soc., 118(45):11225–11236, 1996. [http://dx.doi.org/10.1021/ja9621760 10.1021/ja9621760]. #Jorgensen1985 W. L. Jorgensen and J. D. Madura. ''Temperature and size dependence for Monte-Carlo simulations of TIP4P water''. Mol. Phys., 56(6):1381–1392, December 1985. #Berendsen1981 H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, and J. Hermans. ''Interaction models for water in relation to protein hydration''. In B. Pullman, editor, Intermolecular Forces, page 331. D. Reidel Publishing Company, Dordrecht, Holland, 1981. #Cordes2002 pmid=12417206 #Daura1999 X Daura, K Gademann, B Jaun, D Seebach, WF van Gunsteren, and AE Mark. ''Peptide folding: When simulation meets experiment''. Angewandte Chemie-International Edition, 38 (1-2):236–240, 1999. [http://dx.doi.org/10.1002/(SICI)1521-3773(19990115)38:1/2%3C236::AID-ANIE236%3E3.0.CO;2-M <nowiki>10.1002/(SICI)1521-3773(19990115)38:1/2<236::AID-ANIE236>3.0.CO;2-M</nowiki>]. </biblio> [[Category:Hippo]] [[Category:Software]] d4da0a5535997c8b5b75f55569d1d9fbee13b779 130 121 2008-10-19T15:19:56Z Oliver 2 /* Installing the software */ clarified MPI binaries (after talking to Martin) wikitext text/x-wiki [[Image:Gbim.jpg‎|frame|right|A peptide folds and inserts into a membrane; the membrane is represented by an implicit Generalized Born model.]] '''Hippo''' is a software package for simulation and analysis of bio-molecules at an atomic level. It has been specifically developed for very efficient protein folding studies in aqueous and membrane environments. The code is very fast due to optimized and hand-coded assembly routines which make use of fast multi-media instructions on modern x86 cpus. Hippo is (partially) parallelized (using industry-standard [http://www.openmp.org/ OpenMP]). == Features == === Simulation methods === * [[Molecular dynamics]] (MD) in NVT, NPT, NVE ensembles * Metropolis [[Monte Carlo]] (MC) in NVT and NPT ensembles <cite>JACS2004,JPhysChemB2006</cite> * [[Replica exchange]] with MD and MC === Force fields === * OPLS-AA <cite>Jorgensen1996,Kaminski2001</cite> === Solvation models === * explicit solvent (water: TIP4P <cite>Jorgensen1985</cite>, SPC <cite>Berendsen1981</cite>) * Generalized Born implicit solvent (GB/SA) * Generalized Born implicit membrane (GB/IM) <cite>Proteins2007,BJ2007,Proteins2005</cite> === Enhanced productivity === A number of features make it easy to use Hippo so that one can spend more time on working on problems and less time on setting up structures or dealing with system crashes: * seamless restarts * intelligent pdb structure loader: reads most pdbs, can complete missing atoms, and builds the topology * graphical frontend under development (Windows only) === Analysis === [[Image:Peptidescan.jpg|frame|right|Adiabatic Generalized Born energy surface for different positions and orientations of a helical peptide in a membrane (output from the ''translation+rotation energy scan'' analysis tool).]] A growing number of analysis tools are built into Hippo, for instance ; adiabatic translation+rotation energy scan: determines the Generalized Born energy of a peptide in a membrane <cite>MMB2008,BJ2006</cite>; this allows to decide if a (typically helical) peptide inserts into the membrane and at which depth and angle or if it prefers a surface-bound or even a fully solvated state ; RMSD: calculates the [[RMSD|root mean square deviation]] of trajectory frames to a reference structure ; helicity: degree of helicity of segments along trajectory ; Z - tilt - kink graph: Calculates center of mass, tilt angle, and kink angle of a peptide in a membrane as a function of simulation time. The membrane is in the xy plane, with z = 0 the membrane center. Kink angle is with respect to the membrane normal. <cite>Cordes2002</cite> ; cluster: Performs a cluster analysis using the pairwise method by Daura et al.<cite>Daura1999</cite> ; fit to phase: recenters trajectory on the centre of mass of a phase (such as a lipid membrane) ; fit solute to previous frames: Generate a PDB movie by RMSD fitting the solute of each frame to the previous frame. The Hippo output format is a binary [[File formats#xyz-movie|xyz-movie]] (see the [http://openbabel.org/wiki/XYZ definition of the xyz format]); thus many other [[analysis]] tools can also be used. == Installation == === Download === Binaries are publicly available from the [http://www.biowerkzeug.com/ Biowerkzeg.com download page] for '''Linux''' and '''Windows'''. <!-- , and '''Mac OS X (Intel platform only)'''. --> === Installing the software === Unzip the downloaded file. It will unpack into its own <tt>hippo</tt> directory where you will find * compiled executables (see below) ** <tt>hippo</tt>: the [[#Simulation methods|MD and MC program]] ** <tt>analyse</tt>: the [[#Analysis|analysis program]] * the manual ([http://www.biowerkzeug.de/downloads/hippo/hippo_manual.pdf pdf]) * the [[Hippo license|license]] (to which you consent by downloading) * the OPLS-AA forcefield file (in Hippo format) * the readme.txt file * the <tt>testjobs</tt> directory with example systems {| class="wikitable" align="right" |+Hippo executables !cpu !!Linux !!Windows |- |SSSE3 (Core Duo,...) ||<tt>hippo</tt> ||<tt>hippo.exe</tt> |- |SSE (PIII,P4,Athlon,...) ||<tt>hippo_p3</tt> ||<tt>hippo_p3.exe</tt> |} The package includes binaries that run under Linux and Windows on any Intel or AMD processor that has the SSE or SSSE3 multi media instructions. Depending on your system and needs, choose an executable from the package as shown in the table ''Hippo executables''. If in doubt, simply try them out in order; if it will not run you will receive an error message such as Fatal Error: This program was not built to run on the processor in your system. The allowed processors are: Intel(R) Core(TM) Duo processors and compatible Intel processors with supplemental Streaming SIMD Extensions 3 (SSSE3) instruction support. In this case try the <tt>hippo_p3</tt> or <tt>hippo_p3.exe</tt> executable. If this still doesn't work, [http://forums.biowerkzeug.org/viewforum.php?f=6 post a request in the Hippo Installation forum]. Executables with the <tt>_mpi</tt> extension have been compiled with MPI support (mpich 2) and are only used for replica exchange simulation (REXMD). If you just want to run multithreaded simulations just use the standard binaries (which are all compiled with OpenMP). === Test cases === The <tt>testjobs</tt> directory contains a number of testcases. Run the <tt>calc_testjobs_linux.bat</tt> or <tt>calc_testjobs_win32.bat</tt> script in order to perform ''all'' tests. On modern processors this should take between 2 and 4 Minutes. Use the tests in order to get started in running your own systems. == References == <biblio> #MMB2008 pmid=18428040 #Proteins2007 pmid=17600830 #BJ2007 pmid=17218457 #BJ2006 pmid=16339877 #JPhysChemB2006 pmid=16913813 #Proteins2005 pmid=15723347 #JACS2004 pmid=14871118 #Kaminski2001 George A. Kaminski, Richard A. Friesner, Julian Tirado-Rives, and William L. Jorgensen. ''Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides''. J. Phys. Chem. B, 105(28):6474–6487, 2001. [http://dx.doi.org/10.1021/jp003919d 10.1021/jp003919d]. #Jorgensen1996 W. L. Jorgensen, D. S. Maxwell, and J. Tirado-Rives. ''Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids''. J. Am. Chem. Soc., 118(45):11225–11236, 1996. [http://dx.doi.org/10.1021/ja9621760 10.1021/ja9621760]. #Jorgensen1985 W. L. Jorgensen and J. D. Madura. ''Temperature and size dependence for Monte-Carlo simulations of TIP4P water''. Mol. Phys., 56(6):1381–1392, December 1985. #Berendsen1981 H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, and J. Hermans. ''Interaction models for water in relation to protein hydration''. In B. Pullman, editor, Intermolecular Forces, page 331. D. Reidel Publishing Company, Dordrecht, Holland, 1981. #Cordes2002 pmid=12417206 #Daura1999 X Daura, K Gademann, B Jaun, D Seebach, WF van Gunsteren, and AE Mark. ''Peptide folding: When simulation meets experiment''. Angewandte Chemie-International Edition, 38 (1-2):236–240, 1999. [http://dx.doi.org/10.1002/(SICI)1521-3773(19990115)38:1/2%3C236::AID-ANIE236%3E3.0.CO;2-M <nowiki>10.1002/(SICI)1521-3773(19990115)38:1/2<236::AID-ANIE236>3.0.CO;2-M</nowiki>]. </biblio> [[Category:Hippo]] [[Category:Software]] 2e75d60999be1cfa1d324163a3c688c7edf421b1 131 130 2008-10-19T15:42:13Z Oliver 2 /* Installing the software */ mpich2 link wikitext text/x-wiki [[Image:Gbim.jpg‎|frame|right|A peptide folds and inserts into a membrane; the membrane is represented by an implicit Generalized Born model.]] '''Hippo''' is a software package for simulation and analysis of bio-molecules at an atomic level. It has been specifically developed for very efficient protein folding studies in aqueous and membrane environments. The code is very fast due to optimized and hand-coded assembly routines which make use of fast multi-media instructions on modern x86 cpus. Hippo is (partially) parallelized (using industry-standard [http://www.openmp.org/ OpenMP]). == Features == === Simulation methods === * [[Molecular dynamics]] (MD) in NVT, NPT, NVE ensembles * Metropolis [[Monte Carlo]] (MC) in NVT and NPT ensembles <cite>JACS2004,JPhysChemB2006</cite> * [[Replica exchange]] with MD and MC === Force fields === * OPLS-AA <cite>Jorgensen1996,Kaminski2001</cite> === Solvation models === * explicit solvent (water: TIP4P <cite>Jorgensen1985</cite>, SPC <cite>Berendsen1981</cite>) * Generalized Born implicit solvent (GB/SA) * Generalized Born implicit membrane (GB/IM) <cite>Proteins2007,BJ2007,Proteins2005</cite> === Enhanced productivity === A number of features make it easy to use Hippo so that one can spend more time on working on problems and less time on setting up structures or dealing with system crashes: * seamless restarts * intelligent pdb structure loader: reads most pdbs, can complete missing atoms, and builds the topology * graphical frontend under development (Windows only) === Analysis === [[Image:Peptidescan.jpg|frame|right|Adiabatic Generalized Born energy surface for different positions and orientations of a helical peptide in a membrane (output from the ''translation+rotation energy scan'' analysis tool).]] A growing number of analysis tools are built into Hippo, for instance ; adiabatic translation+rotation energy scan: determines the Generalized Born energy of a peptide in a membrane <cite>MMB2008,BJ2006</cite>; this allows to decide if a (typically helical) peptide inserts into the membrane and at which depth and angle or if it prefers a surface-bound or even a fully solvated state ; RMSD: calculates the [[RMSD|root mean square deviation]] of trajectory frames to a reference structure ; helicity: degree of helicity of segments along trajectory ; Z - tilt - kink graph: Calculates center of mass, tilt angle, and kink angle of a peptide in a membrane as a function of simulation time. The membrane is in the xy plane, with z = 0 the membrane center. Kink angle is with respect to the membrane normal. <cite>Cordes2002</cite> ; cluster: Performs a cluster analysis using the pairwise method by Daura et al.<cite>Daura1999</cite> ; fit to phase: recenters trajectory on the centre of mass of a phase (such as a lipid membrane) ; fit solute to previous frames: Generate a PDB movie by RMSD fitting the solute of each frame to the previous frame. The Hippo output format is a binary [[File formats#xyz-movie|xyz-movie]] (see the [http://openbabel.org/wiki/XYZ definition of the xyz format]); thus many other [[analysis]] tools can also be used. == Installation == === Download === Binaries are publicly available from the [http://www.biowerkzeug.com/ Biowerkzeg.com download page] for '''Linux''' and '''Windows'''. <!-- , and '''Mac OS X (Intel platform only)'''. --> === Installing the software === Unzip the downloaded file. It will unpack into its own <tt>hippo</tt> directory where you will find * compiled executables (see below) ** <tt>hippo</tt>: the [[#Simulation methods|MD and MC program]] ** <tt>analyse</tt>: the [[#Analysis|analysis program]] * the manual ([http://www.biowerkzeug.de/downloads/hippo/hippo_manual.pdf pdf]) * the [[Hippo license|license]] (to which you consent by downloading) * the OPLS-AA forcefield file (in Hippo format) * the readme.txt file * the <tt>testjobs</tt> directory with example systems {| class="wikitable" align="right" |+Hippo executables !cpu !!Linux !!Windows |- |SSSE3 (Core Duo,...) ||<tt>hippo</tt> ||<tt>hippo.exe</tt> |- |SSE (PIII,P4,Athlon,...) ||<tt>hippo_p3</tt> ||<tt>hippo_p3.exe</tt> |} The package includes binaries that run under Linux and Windows on any Intel or AMD processor that has the SSE or SSSE3 multi media instructions. Depending on your system and needs, choose an executable from the package as shown in the table ''Hippo executables''. If in doubt, simply try them out in order; if it will not run you will receive an error message such as Fatal Error: This program was not built to run on the processor in your system. The allowed processors are: Intel(R) Core(TM) Duo processors and compatible Intel processors with supplemental Streaming SIMD Extensions 3 (SSSE3) instruction support. In this case try the <tt>hippo_p3</tt> or <tt>hippo_p3.exe</tt> executable. If this still doesn't work, [http://forums.biowerkzeug.org/viewforum.php?f=6 post a request in the Hippo Installation forum]. Executables with the <tt>_mpi</tt> extension have been compiled with MPI support ([http://www.mcs.anl.gov/research/projects/mpich2/index.php mpich2]) and are only used for replica exchange simulation (REXMD). If you just want to run multithreaded simulations just use the standard binaries (which are all compiled with OpenMP). === Test cases === The <tt>testjobs</tt> directory contains a number of testcases. Run the <tt>calc_testjobs_linux.bat</tt> or <tt>calc_testjobs_win32.bat</tt> script in order to perform ''all'' tests. On modern processors this should take between 2 and 4 Minutes. Use the tests in order to get started in running your own systems. == References == <biblio> #MMB2008 pmid=18428040 #Proteins2007 pmid=17600830 #BJ2007 pmid=17218457 #BJ2006 pmid=16339877 #JPhysChemB2006 pmid=16913813 #Proteins2005 pmid=15723347 #JACS2004 pmid=14871118 #Kaminski2001 George A. Kaminski, Richard A. Friesner, Julian Tirado-Rives, and William L. Jorgensen. ''Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides''. J. Phys. Chem. B, 105(28):6474–6487, 2001. [http://dx.doi.org/10.1021/jp003919d 10.1021/jp003919d]. #Jorgensen1996 W. L. Jorgensen, D. S. Maxwell, and J. Tirado-Rives. ''Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids''. J. Am. Chem. Soc., 118(45):11225–11236, 1996. [http://dx.doi.org/10.1021/ja9621760 10.1021/ja9621760]. #Jorgensen1985 W. L. Jorgensen and J. D. Madura. ''Temperature and size dependence for Monte-Carlo simulations of TIP4P water''. Mol. Phys., 56(6):1381–1392, December 1985. #Berendsen1981 H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, and J. Hermans. ''Interaction models for water in relation to protein hydration''. In B. Pullman, editor, Intermolecular Forces, page 331. D. Reidel Publishing Company, Dordrecht, Holland, 1981. #Cordes2002 pmid=12417206 #Daura1999 X Daura, K Gademann, B Jaun, D Seebach, WF van Gunsteren, and AE Mark. ''Peptide folding: When simulation meets experiment''. Angewandte Chemie-International Edition, 38 (1-2):236–240, 1999. [http://dx.doi.org/10.1002/(SICI)1521-3773(19990115)38:1/2%3C236::AID-ANIE236%3E3.0.CO;2-M <nowiki>10.1002/(SICI)1521-3773(19990115)38:1/2<236::AID-ANIE236>3.0.CO;2-M</nowiki>]. </biblio> [[Category:Hippo]] [[Category:Software]] 536ea3b035f5f292e281cd163b21860b0fb33104 132 131 2008-10-19T15:42:51Z Oliver 2 /* Installing the software */ wikitext text/x-wiki [[Image:Gbim.jpg‎|frame|right|A peptide folds and inserts into a membrane; the membrane is represented by an implicit Generalized Born model.]] '''Hippo''' is a software package for simulation and analysis of bio-molecules at an atomic level. It has been specifically developed for very efficient protein folding studies in aqueous and membrane environments. The code is very fast due to optimized and hand-coded assembly routines which make use of fast multi-media instructions on modern x86 cpus. Hippo is (partially) parallelized (using industry-standard [http://www.openmp.org/ OpenMP]). == Features == === Simulation methods === * [[Molecular dynamics]] (MD) in NVT, NPT, NVE ensembles * Metropolis [[Monte Carlo]] (MC) in NVT and NPT ensembles <cite>JACS2004,JPhysChemB2006</cite> * [[Replica exchange]] with MD and MC === Force fields === * OPLS-AA <cite>Jorgensen1996,Kaminski2001</cite> === Solvation models === * explicit solvent (water: TIP4P <cite>Jorgensen1985</cite>, SPC <cite>Berendsen1981</cite>) * Generalized Born implicit solvent (GB/SA) * Generalized Born implicit membrane (GB/IM) <cite>Proteins2007,BJ2007,Proteins2005</cite> === Enhanced productivity === A number of features make it easy to use Hippo so that one can spend more time on working on problems and less time on setting up structures or dealing with system crashes: * seamless restarts * intelligent pdb structure loader: reads most pdbs, can complete missing atoms, and builds the topology * graphical frontend under development (Windows only) === Analysis === [[Image:Peptidescan.jpg|frame|right|Adiabatic Generalized Born energy surface for different positions and orientations of a helical peptide in a membrane (output from the ''translation+rotation energy scan'' analysis tool).]] A growing number of analysis tools are built into Hippo, for instance ; adiabatic translation+rotation energy scan: determines the Generalized Born energy of a peptide in a membrane <cite>MMB2008,BJ2006</cite>; this allows to decide if a (typically helical) peptide inserts into the membrane and at which depth and angle or if it prefers a surface-bound or even a fully solvated state ; RMSD: calculates the [[RMSD|root mean square deviation]] of trajectory frames to a reference structure ; helicity: degree of helicity of segments along trajectory ; Z - tilt - kink graph: Calculates center of mass, tilt angle, and kink angle of a peptide in a membrane as a function of simulation time. The membrane is in the xy plane, with z = 0 the membrane center. Kink angle is with respect to the membrane normal. <cite>Cordes2002</cite> ; cluster: Performs a cluster analysis using the pairwise method by Daura et al.<cite>Daura1999</cite> ; fit to phase: recenters trajectory on the centre of mass of a phase (such as a lipid membrane) ; fit solute to previous frames: Generate a PDB movie by RMSD fitting the solute of each frame to the previous frame. The Hippo output format is a binary [[File formats#xyz-movie|xyz-movie]] (see the [http://openbabel.org/wiki/XYZ definition of the xyz format]); thus many other [[analysis]] tools can also be used. == Installation == === Download === Binaries are publicly available from the [http://www.biowerkzeug.com/ Biowerkzeg.com download page] for '''Linux''' and '''Windows'''. <!-- , and '''Mac OS X (Intel platform only)'''. --> === Installing the software === Unzip the downloaded file. It will unpack into its own <tt>hippo</tt> directory where you will find * compiled executables (see below) ** <tt>hippo</tt>: the [[#Simulation methods|MD and MC program]] ** <tt>analyse</tt>: the [[#Analysis|analysis program]] * the manual ([http://www.biowerkzeug.de/downloads/hippo/hippo_manual.pdf pdf]) * the [[Hippo license|license]] (to which you consent by downloading) * the OPLS-AA forcefield file (in Hippo format) * the readme.txt file * the <tt>testjobs</tt> directory with example systems {| class="wikitable" align="right" |+Hippo executables !cpu !!Linux !!Windows |- |SSSE3 (Core Duo,...) ||<tt>hippo</tt> ||<tt>hippo.exe</tt> |- |SSE (PIII,P4,Athlon,...) ||<tt>hippo_p3</tt> ||<tt>hippo_p3.exe</tt> |} The package includes binaries that run under Linux and Windows on any Intel or AMD processor that has the SSE or SSSE3 multi media instructions. Depending on your system and needs, choose an executable from the package as shown in the table ''Hippo executables''. If in doubt, simply try them out in order; if it will not run you will receive an error message such as Fatal Error: This program was not built to run on the processor in your system. The allowed processors are: Intel(R) Core(TM) Duo processors and compatible Intel processors with supplemental Streaming SIMD Extensions 3 (SSSE3) instruction support. In this case try the <tt>hippo_p3</tt> or <tt>hippo_p3.exe</tt> executable. If this still doesn't work, [http://forums.biowerkzeug.org/viewforum.php?f=6 post a request in the Hippo Installation forum]. Executables with the <tt>_mpi</tt> extension have been compiled with MPI support ([http://www.mcs.anl.gov/research/projects/mpich2/index.php mpich2]) and are only used for [[replica exchange simulations]] (REXMD). If you just want to run multithreaded simulations just use the standard binaries (which are all compiled with OpenMP). === Test cases === The <tt>testjobs</tt> directory contains a number of testcases. Run the <tt>calc_testjobs_linux.bat</tt> or <tt>calc_testjobs_win32.bat</tt> script in order to perform ''all'' tests. On modern processors this should take between 2 and 4 Minutes. Use the tests in order to get started in running your own systems. == References == <biblio> #MMB2008 pmid=18428040 #Proteins2007 pmid=17600830 #BJ2007 pmid=17218457 #BJ2006 pmid=16339877 #JPhysChemB2006 pmid=16913813 #Proteins2005 pmid=15723347 #JACS2004 pmid=14871118 #Kaminski2001 George A. Kaminski, Richard A. Friesner, Julian Tirado-Rives, and William L. Jorgensen. ''Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides''. J. Phys. Chem. B, 105(28):6474–6487, 2001. [http://dx.doi.org/10.1021/jp003919d 10.1021/jp003919d]. #Jorgensen1996 W. L. Jorgensen, D. S. Maxwell, and J. Tirado-Rives. ''Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids''. J. Am. Chem. Soc., 118(45):11225–11236, 1996. [http://dx.doi.org/10.1021/ja9621760 10.1021/ja9621760]. #Jorgensen1985 W. L. Jorgensen and J. D. Madura. ''Temperature and size dependence for Monte-Carlo simulations of TIP4P water''. Mol. Phys., 56(6):1381–1392, December 1985. #Berendsen1981 H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, and J. Hermans. ''Interaction models for water in relation to protein hydration''. In B. Pullman, editor, Intermolecular Forces, page 331. D. Reidel Publishing Company, Dordrecht, Holland, 1981. #Cordes2002 pmid=12417206 #Daura1999 X Daura, K Gademann, B Jaun, D Seebach, WF van Gunsteren, and AE Mark. ''Peptide folding: When simulation meets experiment''. Angewandte Chemie-International Edition, 38 (1-2):236–240, 1999. [http://dx.doi.org/10.1002/(SICI)1521-3773(19990115)38:1/2%3C236::AID-ANIE236%3E3.0.CO;2-M <nowiki>10.1002/(SICI)1521-3773(19990115)38:1/2<236::AID-ANIE236>3.0.CO;2-M</nowiki>]. </biblio> [[Category:Hippo]] [[Category:Software]] 57c6be44e6a750711405aeecaa4644069cb58cf5 133 132 2008-10-19T15:44:06Z Oliver 2 /* Installing the software */ OpenMP link wikitext text/x-wiki [[Image:Gbim.jpg‎|frame|right|A peptide folds and inserts into a membrane; the membrane is represented by an implicit Generalized Born model.]] '''Hippo''' is a software package for simulation and analysis of bio-molecules at an atomic level. It has been specifically developed for very efficient protein folding studies in aqueous and membrane environments. The code is very fast due to optimized and hand-coded assembly routines which make use of fast multi-media instructions on modern x86 cpus. Hippo is (partially) parallelized (using industry-standard [http://www.openmp.org/ OpenMP]). == Features == === Simulation methods === * [[Molecular dynamics]] (MD) in NVT, NPT, NVE ensembles * Metropolis [[Monte Carlo]] (MC) in NVT and NPT ensembles <cite>JACS2004,JPhysChemB2006</cite> * [[Replica exchange]] with MD and MC === Force fields === * OPLS-AA <cite>Jorgensen1996,Kaminski2001</cite> === Solvation models === * explicit solvent (water: TIP4P <cite>Jorgensen1985</cite>, SPC <cite>Berendsen1981</cite>) * Generalized Born implicit solvent (GB/SA) * Generalized Born implicit membrane (GB/IM) <cite>Proteins2007,BJ2007,Proteins2005</cite> === Enhanced productivity === A number of features make it easy to use Hippo so that one can spend more time on working on problems and less time on setting up structures or dealing with system crashes: * seamless restarts * intelligent pdb structure loader: reads most pdbs, can complete missing atoms, and builds the topology * graphical frontend under development (Windows only) === Analysis === [[Image:Peptidescan.jpg|frame|right|Adiabatic Generalized Born energy surface for different positions and orientations of a helical peptide in a membrane (output from the ''translation+rotation energy scan'' analysis tool).]] A growing number of analysis tools are built into Hippo, for instance ; adiabatic translation+rotation energy scan: determines the Generalized Born energy of a peptide in a membrane <cite>MMB2008,BJ2006</cite>; this allows to decide if a (typically helical) peptide inserts into the membrane and at which depth and angle or if it prefers a surface-bound or even a fully solvated state ; RMSD: calculates the [[RMSD|root mean square deviation]] of trajectory frames to a reference structure ; helicity: degree of helicity of segments along trajectory ; Z - tilt - kink graph: Calculates center of mass, tilt angle, and kink angle of a peptide in a membrane as a function of simulation time. The membrane is in the xy plane, with z = 0 the membrane center. Kink angle is with respect to the membrane normal. <cite>Cordes2002</cite> ; cluster: Performs a cluster analysis using the pairwise method by Daura et al.<cite>Daura1999</cite> ; fit to phase: recenters trajectory on the centre of mass of a phase (such as a lipid membrane) ; fit solute to previous frames: Generate a PDB movie by RMSD fitting the solute of each frame to the previous frame. The Hippo output format is a binary [[File formats#xyz-movie|xyz-movie]] (see the [http://openbabel.org/wiki/XYZ definition of the xyz format]); thus many other [[analysis]] tools can also be used. == Installation == === Download === Binaries are publicly available from the [http://www.biowerkzeug.com/ Biowerkzeg.com download page] for '''Linux''' and '''Windows'''. <!-- , and '''Mac OS X (Intel platform only)'''. --> === Installing the software === Unzip the downloaded file. It will unpack into its own <tt>hippo</tt> directory where you will find * compiled executables (see below) ** <tt>hippo</tt>: the [[#Simulation methods|MD and MC program]] ** <tt>analyse</tt>: the [[#Analysis|analysis program]] * the manual ([http://www.biowerkzeug.de/downloads/hippo/hippo_manual.pdf pdf]) * the [[Hippo license|license]] (to which you consent by downloading) * the OPLS-AA forcefield file (in Hippo format) * the readme.txt file * the <tt>testjobs</tt> directory with example systems {| class="wikitable" align="right" |+Hippo executables !cpu !!Linux !!Windows |- |SSSE3 (Core Duo,...) ||<tt>hippo</tt> ||<tt>hippo.exe</tt> |- |SSE (PIII,P4,Athlon,...) ||<tt>hippo_p3</tt> ||<tt>hippo_p3.exe</tt> |} The package includes binaries that run under Linux and Windows on any Intel or AMD processor that has the SSE or SSSE3 multi media instructions. Depending on your system and needs, choose an executable from the package as shown in the table ''Hippo executables''. If in doubt, simply try them out in order; if it will not run you will receive an error message such as Fatal Error: This program was not built to run on the processor in your system. The allowed processors are: Intel(R) Core(TM) Duo processors and compatible Intel processors with supplemental Streaming SIMD Extensions 3 (SSSE3) instruction support. In this case try the <tt>hippo_p3</tt> or <tt>hippo_p3.exe</tt> executable. If this still doesn't work, [http://forums.biowerkzeug.org/viewforum.php?f=6 post a request in the Hippo Installation forum]. Executables with the <tt>_mpi</tt> extension have been compiled with MPI support ([http://www.mcs.anl.gov/research/projects/mpich2/index.php mpich2]) and are only used for [[replica exchange simulations]] (REXMD). If you just want to run multithreaded simulations just use the standard binaries (which are all compiled with [http://www.openmp.org/ OpenMP]). === Test cases === The <tt>testjobs</tt> directory contains a number of testcases. Run the <tt>calc_testjobs_linux.bat</tt> or <tt>calc_testjobs_win32.bat</tt> script in order to perform ''all'' tests. On modern processors this should take between 2 and 4 Minutes. Use the tests in order to get started in running your own systems. == References == <biblio> #MMB2008 pmid=18428040 #Proteins2007 pmid=17600830 #BJ2007 pmid=17218457 #BJ2006 pmid=16339877 #JPhysChemB2006 pmid=16913813 #Proteins2005 pmid=15723347 #JACS2004 pmid=14871118 #Kaminski2001 George A. Kaminski, Richard A. Friesner, Julian Tirado-Rives, and William L. Jorgensen. ''Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides''. J. Phys. Chem. B, 105(28):6474–6487, 2001. [http://dx.doi.org/10.1021/jp003919d 10.1021/jp003919d]. #Jorgensen1996 W. L. Jorgensen, D. S. Maxwell, and J. Tirado-Rives. ''Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids''. J. Am. Chem. Soc., 118(45):11225–11236, 1996. [http://dx.doi.org/10.1021/ja9621760 10.1021/ja9621760]. #Jorgensen1985 W. L. Jorgensen and J. D. Madura. ''Temperature and size dependence for Monte-Carlo simulations of TIP4P water''. Mol. Phys., 56(6):1381–1392, December 1985. #Berendsen1981 H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, and J. Hermans. ''Interaction models for water in relation to protein hydration''. In B. Pullman, editor, Intermolecular Forces, page 331. D. Reidel Publishing Company, Dordrecht, Holland, 1981. #Cordes2002 pmid=12417206 #Daura1999 X Daura, K Gademann, B Jaun, D Seebach, WF van Gunsteren, and AE Mark. ''Peptide folding: When simulation meets experiment''. Angewandte Chemie-International Edition, 38 (1-2):236–240, 1999. [http://dx.doi.org/10.1002/(SICI)1521-3773(19990115)38:1/2%3C236::AID-ANIE236%3E3.0.CO;2-M <nowiki>10.1002/(SICI)1521-3773(19990115)38:1/2<236::AID-ANIE236>3.0.CO;2-M</nowiki>]. </biblio> [[Category:Hippo]] [[Category:Software]] 6cfb426320627027543b5984e07b0fd6557b9bad 136 133 2008-10-20T22:47:39Z Oliver 2 added latest U&U paper wikitext text/x-wiki [[Image:Gbim.jpg‎|frame|right|A peptide folds and inserts into a membrane; the membrane is represented by an implicit Generalized Born model.]] '''Hippo''' is a software package for simulation and analysis of bio-molecules at an atomic level. It has been specifically developed for very efficient protein folding studies in aqueous and membrane environments. The code is very fast due to optimized and hand-coded assembly routines which make use of fast multi-media instructions on modern x86 cpus. Hippo is (partially) parallelized (using industry-standard [http://www.openmp.org/ OpenMP]). == Features == === Simulation methods === * [[Molecular dynamics]] (MD) in NVT, NPT, NVE ensembles <cite>Proteins2008</cite> * Metropolis [[Monte Carlo]] (MC) in NVT and NPT ensembles <cite>JACS2004,JPhysChemB2006</cite> * [[Replica exchange]] with MD and MC <cite>Proteins2007</cite> === Force fields === * OPLS-AA <cite>Jorgensen1996,Kaminski2001</cite> === Solvation models === * explicit solvent (water: TIP4P <cite>Jorgensen1985</cite>, SPC <cite>Berendsen1981</cite>) * Generalized Born implicit solvent (GB/SA) * Generalized Born implicit membrane (GB/IM) <cite>Proteins2008,Proteins2007,BJ2007,Proteins2005</cite> === Enhanced productivity === A number of features make it easy to use Hippo so that one can spend more time on working on problems and less time on setting up structures or dealing with system crashes: * seamless restarts * intelligent pdb structure loader: reads most pdbs, can complete missing atoms, and builds the topology * graphical frontend under development (Windows only) === Analysis === [[Image:Peptidescan.jpg|frame|right|Adiabatic Generalized Born energy surface for different positions and orientations of a helical peptide in a membrane (output from the ''translation+rotation energy scan'' analysis tool).]] A growing number of analysis tools are built into Hippo, for instance ; adiabatic translation+rotation energy scan: determines the Generalized Born energy of a peptide in a membrane <cite>MMB2008,BJ2006</cite>; this allows to decide if a (typically helical) peptide inserts into the membrane and at which depth and angle or if it prefers a surface-bound or even a fully solvated state ; RMSD: calculates the [[RMSD|root mean square deviation]] of trajectory frames to a reference structure ; helicity: degree of helicity of segments along trajectory ; Z - tilt - kink graph: Calculates center of mass, tilt angle, and kink angle of a peptide in a membrane as a function of simulation time. The membrane is in the xy plane, with z = 0 the membrane center. Kink angle is with respect to the membrane normal. <cite>Cordes2002</cite> ; cluster: Performs a cluster analysis using the pairwise method by Daura et al.<cite>Daura1999</cite> ; fit to phase: recenters trajectory on the centre of mass of a phase (such as a lipid membrane) ; fit solute to previous frames: Generate a PDB movie by RMSD fitting the solute of each frame to the previous frame. The Hippo output format is a binary [[File formats#xyz-movie|xyz-movie]] (see the [http://openbabel.org/wiki/XYZ definition of the xyz format]); thus many other [[analysis]] tools can also be used. == Installation == === Download === Binaries are publicly available from the [http://www.biowerkzeug.com/ Biowerkzeg.com download page] for '''Linux''' and '''Windows'''. <!-- , and '''Mac OS X (Intel platform only)'''. --> === Installing the software === Unzip the downloaded file. It will unpack into its own <tt>hippo</tt> directory where you will find * compiled executables (see below) ** <tt>hippo</tt>: the [[#Simulation methods|MD and MC program]] ** <tt>analyse</tt>: the [[#Analysis|analysis program]] * the manual ([http://www.biowerkzeug.de/downloads/hippo/hippo_manual.pdf pdf]) * the [[Hippo license|license]] (to which you consent by downloading) * the OPLS-AA forcefield file (in Hippo format) * the readme.txt file * the <tt>testjobs</tt> directory with example systems {| class="wikitable" align="right" |+Hippo executables !cpu !!Linux !!Windows |- |SSSE3 (Core Duo,...) ||<tt>hippo</tt> ||<tt>hippo.exe</tt> |- |SSE (PIII,P4,Athlon,...) ||<tt>hippo_p3</tt> ||<tt>hippo_p3.exe</tt> |} The package includes binaries that run under Linux and Windows on any Intel or AMD processor that has the SSE or SSSE3 multi media instructions. Depending on your system and needs, choose an executable from the package as shown in the table ''Hippo executables''. If in doubt, simply try them out in order; if it will not run you will receive an error message such as Fatal Error: This program was not built to run on the processor in your system. The allowed processors are: Intel(R) Core(TM) Duo processors and compatible Intel processors with supplemental Streaming SIMD Extensions 3 (SSSE3) instruction support. In this case try the <tt>hippo_p3</tt> or <tt>hippo_p3.exe</tt> executable. If this still doesn't work, [http://forums.biowerkzeug.org/viewforum.php?f=6 post a request in the Hippo Installation forum]. Executables with the <tt>_mpi</tt> extension have been compiled with MPI support ([http://www.mcs.anl.gov/research/projects/mpich2/index.php mpich2]) and are only used for [[replica exchange simulations]] (REXMD). If you just want to run multithreaded simulations just use the standard binaries (which are all compiled with [http://www.openmp.org/ OpenMP]). === Test cases === The <tt>testjobs</tt> directory contains a number of testcases. Run the <tt>calc_testjobs_linux.bat</tt> or <tt>calc_testjobs_win32.bat</tt> script in order to perform ''all'' tests. On modern processors this should take between 2 and 4 Minutes. Use the tests in order to get started in running your own systems. == References == <biblio> #MMB2008 pmid=18428040 #Proteins2007 pmid=17600830 #BJ2007 pmid=17218457 #BJ2006 pmid=16339877 #JPhysChemB2006 pmid=16913813 #Proteins2005 pmid=15723347 #JACS2004 pmid=14871118 #Kaminski2001 George A. Kaminski, Richard A. Friesner, Julian Tirado-Rives, and William L. Jorgensen. ''Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides''. J. Phys. Chem. B, 105(28):6474–6487, 2001. [http://dx.doi.org/10.1021/jp003919d 10.1021/jp003919d]. #Jorgensen1996 W. L. Jorgensen, D. S. Maxwell, and J. Tirado-Rives. ''Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids''. J. Am. Chem. Soc., 118(45):11225–11236, 1996. [http://dx.doi.org/10.1021/ja9621760 10.1021/ja9621760]. #Jorgensen1985 W. L. Jorgensen and J. D. Madura. ''Temperature and size dependence for Monte-Carlo simulations of TIP4P water''. Mol. Phys., 56(6):1381–1392, December 1985. #Berendsen1981 H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, and J. Hermans. ''Interaction models for water in relation to protein hydration''. In B. Pullman, editor, Intermolecular Forces, page 331. D. Reidel Publishing Company, Dordrecht, Holland, 1981. #Cordes2002 pmid=12417206 #Daura1999 X Daura, K Gademann, B Jaun, D Seebach, WF van Gunsteren, and AE Mark. ''Peptide folding: When simulation meets experiment''. Angewandte Chemie-International Edition, 38 (1-2):236–240, 1999. [http://dx.doi.org/10.1002/(SICI)1521-3773(19990115)38:1/2%3C236::AID-ANIE236%3E3.0.CO;2-M <nowiki>10.1002/(SICI)1521-3773(19990115)38:1/2<236::AID-ANIE236>3.0.CO;2-M</nowiki>]. #Proteins2008 Jakob P. Ulmschneider and Martin B. Ulmschneider. ''Sampling efficiency in explicit and implicit membrane environments studied by peptide folding simulations''. Proteins [http://dx.doi.org/10.1002/prot.22270 10.1002/prot.22270]. </biblio> [[Category:Hippo]] [[Category:Software]] 599ffb37a76f32d7c006dab2cdb9e94f1feae009 140 136 2008-11-13T13:49:05Z Kaihsu 10 /* Features */ wikitext text/x-wiki [[Image:Gbim.jpg‎|frame|right|A peptide folds and inserts into a membrane; the membrane is represented by an implicit Generalized Born model.]] '''Hippo''' is a software package for simulation and analysis of bio-molecules at an atomic level. It has been specifically developed for very efficient protein folding studies in aqueous and membrane environments. The code is very fast due to optimized and hand-coded assembly routines which make use of fast multi-media instructions on modern x86 cpus. Hippo is (partially) parallelized (using industry-standard [http://www.openmp.org/ OpenMP]). == Features == [[Image:Hippopotamus.jpg|thumb|right|Not this hippo.]] === Simulation methods === * [[Molecular dynamics]] (MD) in NVT, NPT, NVE ensembles <cite>Proteins2008</cite> * Metropolis [[Monte Carlo]] (MC) in NVT and NPT ensembles <cite>JACS2004,JPhysChemB2006</cite> * [[Replica exchange]] with MD and MC <cite>Proteins2007</cite> === Force fields === * OPLS-AA <cite>Jorgensen1996,Kaminski2001</cite> === Solvation models === * explicit solvent (water: TIP4P <cite>Jorgensen1985</cite>, SPC <cite>Berendsen1981</cite>) * Generalized Born implicit solvent (GB/SA) * Generalized Born implicit membrane (GB/IM) <cite>Proteins2008,Proteins2007,BJ2007,Proteins2005</cite> === Enhanced productivity === A number of features make it easy to use Hippo so that one can spend more time on working on problems and less time on setting up structures or dealing with system crashes: * seamless restarts * intelligent pdb structure loader: reads most pdbs, can complete missing atoms, and builds the topology * graphical frontend under development (Windows only) === Analysis === [[Image:Peptidescan.jpg|frame|right|Adiabatic Generalized Born energy surface for different positions and orientations of a helical peptide in a membrane (output from the ''translation+rotation energy scan'' analysis tool).]] A growing number of analysis tools are built into Hippo, for instance ; adiabatic translation+rotation energy scan: determines the Generalized Born energy of a peptide in a membrane <cite>MMB2008,BJ2006</cite>; this allows to decide if a (typically helical) peptide inserts into the membrane and at which depth and angle or if it prefers a surface-bound or even a fully solvated state ; RMSD: calculates the [[RMSD|root mean square deviation]] of trajectory frames to a reference structure ; helicity: degree of helicity of segments along trajectory ; Z - tilt - kink graph: Calculates center of mass, tilt angle, and kink angle of a peptide in a membrane as a function of simulation time. The membrane is in the xy plane, with z = 0 the membrane center. Kink angle is with respect to the membrane normal. <cite>Cordes2002</cite> ; cluster: Performs a cluster analysis using the pairwise method by Daura et al.<cite>Daura1999</cite> ; fit to phase: recenters trajectory on the centre of mass of a phase (such as a lipid membrane) ; fit solute to previous frames: Generate a PDB movie by RMSD fitting the solute of each frame to the previous frame. The Hippo output format is a binary [[File formats#xyz-movie|xyz-movie]] (see the [http://openbabel.org/wiki/XYZ definition of the xyz format]); thus many other [[analysis]] tools can also be used. == Installation == === Download === Binaries are publicly available from the [http://www.biowerkzeug.com/ Biowerkzeg.com download page] for '''Linux''' and '''Windows'''. <!-- , and '''Mac OS X (Intel platform only)'''. --> === Installing the software === Unzip the downloaded file. It will unpack into its own <tt>hippo</tt> directory where you will find * compiled executables (see below) ** <tt>hippo</tt>: the [[#Simulation methods|MD and MC program]] ** <tt>analyse</tt>: the [[#Analysis|analysis program]] * the manual ([http://www.biowerkzeug.de/downloads/hippo/hippo_manual.pdf pdf]) * the [[Hippo license|license]] (to which you consent by downloading) * the OPLS-AA forcefield file (in Hippo format) * the readme.txt file * the <tt>testjobs</tt> directory with example systems {| class="wikitable" align="right" |+Hippo executables !cpu !!Linux !!Windows |- |SSSE3 (Core Duo,...) ||<tt>hippo</tt> ||<tt>hippo.exe</tt> |- |SSE (PIII,P4,Athlon,...) ||<tt>hippo_p3</tt> ||<tt>hippo_p3.exe</tt> |} The package includes binaries that run under Linux and Windows on any Intel or AMD processor that has the SSE or SSSE3 multi media instructions. Depending on your system and needs, choose an executable from the package as shown in the table ''Hippo executables''. If in doubt, simply try them out in order; if it will not run you will receive an error message such as Fatal Error: This program was not built to run on the processor in your system. The allowed processors are: Intel(R) Core(TM) Duo processors and compatible Intel processors with supplemental Streaming SIMD Extensions 3 (SSSE3) instruction support. In this case try the <tt>hippo_p3</tt> or <tt>hippo_p3.exe</tt> executable. If this still doesn't work, [http://forums.biowerkzeug.org/viewforum.php?f=6 post a request in the Hippo Installation forum]. Executables with the <tt>_mpi</tt> extension have been compiled with MPI support ([http://www.mcs.anl.gov/research/projects/mpich2/index.php mpich2]) and are only used for [[replica exchange simulations]] (REXMD). If you just want to run multithreaded simulations just use the standard binaries (which are all compiled with [http://www.openmp.org/ OpenMP]). === Test cases === The <tt>testjobs</tt> directory contains a number of testcases. Run the <tt>calc_testjobs_linux.bat</tt> or <tt>calc_testjobs_win32.bat</tt> script in order to perform ''all'' tests. On modern processors this should take between 2 and 4 Minutes. Use the tests in order to get started in running your own systems. == References == <biblio> #MMB2008 pmid=18428040 #Proteins2007 pmid=17600830 #BJ2007 pmid=17218457 #BJ2006 pmid=16339877 #JPhysChemB2006 pmid=16913813 #Proteins2005 pmid=15723347 #JACS2004 pmid=14871118 #Kaminski2001 George A. Kaminski, Richard A. Friesner, Julian Tirado-Rives, and William L. Jorgensen. ''Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides''. J. Phys. Chem. B, 105(28):6474–6487, 2001. [http://dx.doi.org/10.1021/jp003919d 10.1021/jp003919d]. #Jorgensen1996 W. L. Jorgensen, D. S. Maxwell, and J. Tirado-Rives. ''Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids''. J. Am. Chem. Soc., 118(45):11225–11236, 1996. [http://dx.doi.org/10.1021/ja9621760 10.1021/ja9621760]. #Jorgensen1985 W. L. Jorgensen and J. D. Madura. ''Temperature and size dependence for Monte-Carlo simulations of TIP4P water''. Mol. Phys., 56(6):1381–1392, December 1985. #Berendsen1981 H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, and J. Hermans. ''Interaction models for water in relation to protein hydration''. In B. Pullman, editor, Intermolecular Forces, page 331. D. Reidel Publishing Company, Dordrecht, Holland, 1981. #Cordes2002 pmid=12417206 #Daura1999 X Daura, K Gademann, B Jaun, D Seebach, WF van Gunsteren, and AE Mark. ''Peptide folding: When simulation meets experiment''. Angewandte Chemie-International Edition, 38 (1-2):236–240, 1999. [http://dx.doi.org/10.1002/(SICI)1521-3773(19990115)38:1/2%3C236::AID-ANIE236%3E3.0.CO;2-M <nowiki>10.1002/(SICI)1521-3773(19990115)38:1/2<236::AID-ANIE236>3.0.CO;2-M</nowiki>]. #Proteins2008 Jakob P. Ulmschneider and Martin B. Ulmschneider. ''Sampling efficiency in explicit and implicit membrane environments studied by peptide folding simulations''. Proteins [http://dx.doi.org/10.1002/prot.22270 10.1002/prot.22270]. </biblio> [[Category:Hippo]] [[Category:Software]] 101bec7b9d0e2c1f9e1e2177446385fbd4b93ca7 6 41 102 2008-10-03T10:21:49Z Oliver 2 Output from the trans+rot-scan in Hippo: The adiabatic free energy surface for placing a helical peptide into an implicit Born membrane. wikitext text/x-wiki Output from the trans+rot-scan in Hippo: The adiabatic free energy surface for placing a helical peptide into an implicit Born membrane. b2c93200f9be8137dac6044547842998d181561f 6 42 105 2008-10-03T10:29:16Z Oliver 2 Folding and insertion of a peptide into a implicit Generalized Born membrane. wikitext text/x-wiki Folding and insertion of a peptide into a implicit Generalized Born membrane. a5d0d5a546d4a0597b01ad0f6dace6fb0bc22458 14 43 111 2008-10-08T09:19:09Z Oliver 2 stub wikitext text/x-wiki [[Hippo]] is a software to perform classical atomistic simulations of biomolecules. [[Biowerkzeug_Wiki:About|This wiki]] and the [http://forums.biowerkzeug.org/ Biowerkzeug Forum] are the Hippo communities repository for help and exchange of ideas. Pages in the '''Hippo''' category contain information directly related to Hippo. 215218d9b4b672187b8cbd0dd777f753462c2c96 0 44 113 2008-10-17T21:41:03Z Orbeckst 7 hippo-license.txt (from r26) wikitext text/x-wiki License agreement for HIPPO Beta Biowerkzeug Limited www.biowerkzeug.com BIOWERKZEUG LIMITED IS WILLING TO LICENSE THE HIPPO SOFTWARE AND ACCOMPANYING DOCUMENTATION (COLLECTIVELY, "SOFTWARE") UPON THE CONDITION THAT YOU ACCEPT ALL OF THE TERMS OF THIS LICENSE AGREEMENT ("AGREEMENT"). PLEASE READ THESE TERMS CAREFULLY BEFORE INSTALLING OR USING THE SOFTWARE. BY INSTALLING OR USING THE SOFTWARE, YOU ARE CONSENTING TO BE BOUND BY AND ARE BECOMING A PARTY TO THIS AGREEMENT. IF YOU DO NOT AGREE TO ALL OF THE TERMS OF THIS AGREEMENT, BIOWERKZEUG LIMITED IS UNWILLING TO LICENSE THE SOFTWARE TO YOU ("YOU"), AND YOU SHOULD NOT INSTALL OR USE THE SOFTWARE. TYPES OF LICENSES In order to install and use the Software, You must obtain one of the following two types of licenses: (1) Non-Commercial Use License or (2) Commercial Use License. GRANT OF LICENSE You may use the Software only under one of the following two types of licenses at any time: 1. NON-COMMERCIAL USE LICENSE Provided that you qualify for a Non-Commercial Use License as specified above, and subject to the terms and conditions contained herein, Biowerkzeug Limited hereby grants You, an end user, a personal, non- transferable, non-exclusive, non- sublicensable license to install and use the Software, free of charge, for non-commercial purposes only. 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In the case of any conflict between the terms of this Agreement and the provisions of any purchase order for the Software, the terms of this Agreement shall control. 9a4d3c17bd56cc1006a526658aa98e41d34969b1 8 8 117 23 2008-10-17T22:04:30Z Oliver 2 copied table stuff from http://meta.wikimedia.org/wiki/MediaWiki:Common.css css text/css /* CSS placed here will be applied to all skins */ /* Copied from http://de.wikipedia.org/wiki/MediaWiki:Common.css : "+++++ 3. NEUE [[Hauptseite|HAUPTSEITE]] (ab 2006) +++++" */ /* Kategorie verbergen */ body.page-Hauptseite #catlinks { display:none; } #hauptseite h2 { background-color: #d8e8ff; border: 1px solid #8898bf; font-size: 1em; font-weight: bold; margin-top: 0; margin-bottom: 0; padding-top: 0.1em; padding-bottom: 0.1em; } #hauptseite .inhalt { background-color: #ffffff; border: 1px solid #8898bf; border-top: 0px solid white; padding: 0.3em 0.8em 0.4em 0.8em; } #hauptseite .inhalt hr { background-color: #8898bf; color: #8898bf; height: 1px; margin:0.5em 0; padding: 0; } #hauptseite .inhalt .mehr { clear: both; font-size: 95%; margin-top: 0.8em; text-align: right; } .hauptseite-oben, .hauptseite-links, .hauptseite-rechts { margin-bottom: 1em; } .hauptseite-links { margin-right: 0.5em; } .hauptseite-rechts { margin-left: 0.5em; } .hauptseite-oben h2, .hauptseite-unten h2 { text-align: center; } .hauptseite-oben .inhalt .portale { font-weight: bold; margin-top: 0.2em; margin-bottom: 0.2em; } .hauptseite-oben .inhalt .intern { font-size: 90%; text-align: center; } .hauptseite-links h2, .hauptseite-rechts h2 { text-indent: 0.8em; } #hauptseite-schwesterprojekte .inhalt a { font-weight: bold; } /* p.catlinks span a[href*="/wiki/Kategorie:Arbeitskategorie"] { display:none } wegen HIDDENCAT nicht mehr notwendig */ /* Remove underline from IPA links */ .IPA a:link, .IPA a:visited { text-decoration: none; } span.Unicode { font-family: 'Code2000', 'Sun-ExtA', 'Arial Unicode MS', 'NSimSun', sans-serif; } span.Unicode1 { font-family: 'Code2001', 'Quivira', 'MPH 2B Damase', sans-serif; } span.Unicode2 { font-family: 'Sun-ExtB', 'Code2002', sans-serif; } span.IPA { font-family: 'Quivira', 'Code2000', 'Sun-ExtA', 'DejaVu Sans', 'Gentium', 'Arial Unicode MS', 'Lucida Sans Unicode', sans-serif; } span.IAST { font-family: 'Code2000', 'SunExtA', 'Arial Unicode MS', sans-serif; } span.altitalisch { font-family: 'Quivira', 'Code2001', 'MPH 2B Damase', sans-serif; } span.gotisch { font-family: 'Quivira', 'Code2001', 'MPH 2B Damase', sans-serif; } span.hebrew { font-family: 'Quivira', 'Sun-ExtA', 'Arial Unicode MS', 'SBL Hebrew', 'Code2000', 'MPH 2B Damase', sans-serif; } span.spanAr { font-family: 'Arial Unicode MS', 'Code2000', 'MPH 2B Damase', 'DejaVu Sans', sans-serif; } span.music-symbol { font-family: 'Musical Symbols', 'Euterpe', 'Code2001', sans-serif; } /* Standardmäßige Ausblendung der Flagged-Revisions-Backlog-Sitenotice */ #mw-oldreviewed-notice { display: none; } /* copied from http://meta.wikimedia.org/wiki/MediaWiki:Common.css */ /***** ** Table formatting *****/ table.wikitable, table.prettytable { margin:1em 1em 1em 0; background:#F9F9F9; border:1px #AAA solid; border-collapse:collapse; } table.wikitable th, table.wikitable td, table.prettytable th, table.prettytable td { border:1px #AAA solid; padding:0.2em; } table.wikitable th, table.prettytable th { background:#F2F2F2; text-align:center; } table.wikitable caption, table.prettytable caption { margin-left:inherit; margin-right:inherit; } /***** ** box formatting *****/ .infobox { float:right; clear:right; margin-bottom:0.5em; margin-left:1em; padding:0.2em; border:1px solid #AAA; background:#F9F9F9; color:black; } .infobox td, .infobox th { vertical-align:top; } .infobox caption { font-size:larger; margin-left:inherit; } .infobox.bordered { border-collapse:collapse; } .infobox.bordered td, .infobox.bordered th { border:1px solid #AAA; } .infobox.bordered .borderless td, .infobox.bordered .borderless th { border:0; } /* Change the external link icon to an Adobe icon for all PDF files */ /* (in browsers that support these CSS selectors, like Mozilla and Opera) */ #bodyContent a[href$=".pdf"].external, #bodyContent a[href*=".pdf?"].external, #bodyContent a[href*=".pdf#"].external, #bodyContent a[href$=".PDF"].external, #bodyContent a[href*=".PDF?"].external, #bodyContent a[href*=".PDF#"].external { background: url(http://upload.wikimedia.org/wikipedia/commons/thumb/2/23/Icons-mini-file_acrobat.gif/15px-Icons-mini-file_acrobat.gif) center right no-repeat; padding-right: 16px; } /* Change the external link icon to an Adobe icon anywhere the PDFlink class */ /* is used (notably Template:PDFlink). This works in IE, unlike the above. */ span.PDFlink a { background: url(http://upload.wikimedia.org/wikipedia/commons/thumb/2/23/Icons-mini-file_acrobat.gif/15px-Icons-mini-file_acrobat.gif) center right no-repeat !important; padding-right: 17px !important; } 01a33818e3c420b053099fb614fb19976a2816b4 0 45 122 2008-10-18T04:33:17Z Oliver 2 basic input files wikitext text/x-wiki Overview over files used by [[Hippo]]. * input file ''hippo_input.txt'' * force field ''oplsaa_forcefield.dat'' * topology building blocks ''hippo_protein_database.dat'' * pdb file 3640a4839b5c5815fe4dd78cbe32a868c2aebdfd 123 122 2008-10-18T04:33:51Z Oliver 2 wikitext text/x-wiki Overview over files used by [[Hippo]]. * input file ''hippo_input.txt'' * force field ''oplsaa_forcefield.dat'' * topology building blocks ''hippo_protein_database.dat'' * pdb file [[Category:Hippo]] b96e57027a6cd9f6a65a8d154dde32424270592c 124 123 2008-10-18T20:01:36Z Oliver 2 input file wikitext text/x-wiki Overview over files used by [[Hippo]]. * input file ''hippo_input.txt'' * force field ''oplsaa_forcefield.dat'' * topology building blocks ''hippo_protein_database.dat'' * pdb file == Command input file == Hippo's actions are controlled by the command input file, '''hippo_input.txt'''. It controls what kind of simulation is run, where the coordinates are loaded from, and which parameters are to be used. The input file is '''row/column fixed format''', which means that lines denoting parameters have to be always in the same order in the input file (you can't leave any rows out!) and that parameter values always have to start in the correct column. The sanest way of writing an input file is to use an example input file from the <tt>test</tt> directory and modify the parameter values. [[Category:Hippo]] 6052b7fe1f9d567513a13ada1aba3fd02b2436fc 0 46 125 2008-10-18T20:11:59Z Oliver 2 basic outline of how to run simulations wikitext text/x-wiki This page should help you running simulations with [[Hippo]]. To run a simulation you will need * hippo executable and data files in a directory which we will denote by HIPPO_HOME * a pdb file for your system * a [[Files#Command input file|hippo_input.txt]] The standard protocol is: # make a working directory # copy your input files (pdb and hippo_input.txt) into the working dir # (optional) copy your executable to the dir # start hippo <pre>hippo</pre> Hippo will load the pdb, build an internal topology, and then run the simulation. It will inform of its progress and its estimated finishing time. If there are problems, look at the <tt>log.txt</tt> output file. [[Category:Hippo]] [[Category:Howto]] 972b0dd5db4c1a23cecd454b4b9c3f0fb2216b8f 126 125 2008-10-18T20:13:44Z Oliver 2 wikitext text/x-wiki This page should help you running simulations with [[Hippo]]. To run a simulation you will need * hippo executable and data files in a directory which we will denote by HIPPO_HOME * a pdb file for your system * a [[Files#Command input file|hippo_input.txt]] The standard protocol is: # make a working directory # copy your input files (pdb and hippo_input.txt) into the working dir # copy the hippo data files (<tt>oplsaa_forcefield.dat</tt> and <tt>hippo_protein_database.dat</tt>) into the working dir # (optional) copy your executable into the working dir # start hippo <pre>hippo</pre> Hippo will load the pdb, build an internal topology, and then run the simulation. It will inform of its progress and its estimated finishing time. If there are problems, look at the <tt>log.txt</tt> output file. [[Category:Hippo]] [[Category:Howto]] 5e37f3f031dfb0253eb848a1dfceaf07b2358f46 127 126 2008-10-18T20:14:09Z Oliver 2 wikitext text/x-wiki This page should help you running simulations with [[Hippo]]. To run a simulation you will need * hippo executable and data files in a directory which we will denote by HIPPO_HOME * a pdb file for your system * a [[Files#Command input file|hippo_input.txt]] The standard protocol is: # make a working directory # copy your input files (pdb and <tt>hippo_input.txt</tt>) into the working dir # copy the hippo data files (<tt>oplsaa_forcefield.dat</tt> and <tt>hippo_protein_database.dat</tt>) into the working dir # (optional) copy your executable into the working dir # start hippo <pre>hippo</pre> Hippo will load the pdb, build an internal topology, and then run the simulation. It will inform of its progress and its estimated finishing time. If there are problems, look at the <tt>log.txt</tt> output file. [[Category:Hippo]] [[Category:Howto]] 1dfff8cbc941f036cba84f74420513771cc7d21d 128 127 2008-10-18T20:15:30Z Oliver 2 -> bash script wikitext text/x-wiki This page should help you running simulations with [[Hippo]]. To run a simulation you will need * hippo executable and data files in a directory which we will denote by HIPPO_HOME * a pdb file for your system * a [[Files#Command input file|hippo_input.txt]] The standard protocol is: # make a working directory # copy your input files (pdb and <tt>hippo_input.txt</tt>) into the working dir # copy the hippo data files (<tt>oplsaa_forcefield.dat</tt> and <tt>hippo_protein_database.dat</tt>) into the working dir # (optional) copy your executable into the working dir # start hippo <pre>hippo</pre> Hippo will load the pdb, build an internal topology, and then run the simulation. It will inform of its progress and its estimated finishing time. If there are problems, look at the <tt>log.txt</tt> output file. Steps 1-4 can be automated with the bash script [[hippo_setup.sh]]. [[Category:Hippo]] [[Category:Howto]] 973fb5643cb86b479f2acc4056ef2cda0771f60b 0 47 129 2008-10-18T20:30:08Z Oliver 2 script and example usage wikitext text/x-wiki The '''hippo_setup.sh''' bash script [http://forums.biowerkzeug.org/viewtopic.php?f=2&t=23 automates] the [[Simulations|setup of hippo simulations]]. Copy and paste the script below into a file, name it <tt>setup_hippo.sh</tt>, make it executable, install it in your PATH. Set the variable <tt>HIPPO_HOME</tt> to the directory that you got when unpacking the downloaded hippo.zip file. Example use: hippo_setup.sh -w ProteinX_GBSA_MC ${HIPPO_HOME}/testjobs/test/trpzip2_GBSA_MC/hippo_input.txt ../coord/protein_X.pdb This would * create the working directory ''ProteinX_GBSA_MC'' (and because of the ''-w'' (`wipe') option it would delete everything in this directory before copying files) * copy data files * copy a working executable (the ''-m'' (mpi) option would indicate that we want an executable that can run in parallel) * copy a template for the input file ''hippo_input.txt'' from one of the test jobs * copy the protein structure Then you would edit the command input file ''ProteinX_GBSA_MC/hippo_input.txt'' to suit your needs. Finally, run hippo: ./hippo <pre>#!/bin/bash # Copyright (c) 2008 Oliver Beckstein <orbeckst@gmail.com> # This script is made available under the terms of the GNU Public License v2. # http://www.gnu.org/licenses/gpl-2.0.html#SEC1 # # # prepare for a hippo run by setting up the local working directory #------------------------------------------------------------ # CUSTOMIZATION # - set HIPPO_HOME to the directory where the hippo executables and # support files are located, eg '${HOME}/hippo' # - put this script somewhere into your PATH # : ${HIPPO_HOME:="${HOME}/Library/hippo"} # #------------------------------------------------------------ # # HIPPO_HOME can be set from environment or commandline -D HIPPO_HOME #: ${HIPPO_HOME:=$(dirname "$0")/../hippo_r26} usage="$0 [options] work_dir [input_files ...] This script sets up the work_dir for a run of hippo. work_dir is created unless it exists already. It hard-links the hippo executable and the data files into the directory. Options: -h help -D HIPPO_HOME directory where hippo and files reside -m look for mpi-enabled binaries -w wipe the work_dir ('rm -rf work_dir') before setting up making sure that we start from a clean slate " function die () { local msg="$1" err=${2:-1} echo 1>&2 "ERROR: $msg [status=$err]" exit $err } function pick_binary () { # find working executable # we'll use the first one that only complains about missing input file local hippo_dir="$1" use_mpi="$2" local _hippo_binaries="hippo hippo_p3" local hippo="not_found" local tmpdir=`mktemp -d` pushd >/dev/null "$tmpdir" || die "Failed to set up testing area" for h in ${_hippo_binaries}; do if [ "${use_mpi}" = 1 ]; then exe="${hippo_dir}/${h}_mpi" else exe="${hippo_dir}/${h}" fi if ${exe} 2>&1 | egrep "Could not open file: hippo_input.txt" >/dev/null; then hippo=${exe} break fi done if [ "${hippo}" = "not_found" ]; then ARCH=$(uname -m); OS=$(uname -s); die "No usable hippo executable found (MPI=${use_mpi}); see if there is one at http://www.biowerkzeug.com for your architecture ${ARCH} and operating system ${OS}. " fi popd >/dev/null rm -r "${tmpdir}" || die "Failed to remove tmpdir... weird" echo "${hippo}" return 0 } #set -x # defaults USE_MPI=0 WIPE_WORK_DIR=0 # arg processing TEMP=`getopt -o hmwD: -n 'hippo_setup.sh' -- "$@"` opterr=$? [ $opterr != 0 ] && die "Error parsing the commandline." $opterr eval set -- "$TEMP" while true; do case "$1" in -h) echo -e "${usage}"; exit 0;; -D) HIPPO_HOME="$2"; shift;; -m) USE_MPI=1;; -w) WIPE_WORK_DIR=1;; --) shift; break;; esac shift done [ -d "${HIPPO_HOME}" ] || die "HIPPO_HOME=${HIPPO_HOME} not found" 1 HIPPO_EXE=`pick_binary "${HIPPO_HOME}" ${USE_MPI}` HIPPO_TOPOLOGY="${HIPPO_HOME}/hippo_protein_database.dat" HIPPO_FF="${HIPPO_HOME}/oplsaa_forcefield.dat" test -n "${HIPPO_EXE}" || die "No hippo executable found. Did you set HIPPO_HOME or the -D option?" function setup_hippo () { cp -lf ${HIPPO_EXE} ./hippo && chmod a+x ./hippo || return 1 cp -lf ${HIPPO_TOPOLOGY} . || return 2 cp -lf ${HIPPO_FF} . || return 3 return 0 } WORK_DIR="$1" shift INPUTFILES="$*" test -n "${WORK_DIR}" || die "No work_dir, see $0 -h for help" echo "Setting up Hippo run" echo "------------------------------------------------------------" echo "working directory ${WORK_DIR}" echo "HIPPO_HOME ${HIPPO_HOME}" echo "executable ${HIPPO_EXE} --> ./hippo" echo "force field ${HIPPO_FF}" echo "topology ${HIPPO_TOPOLOGY}" echo "------------------------------------------------------------" echo "additional files ${INPUTFILES}" echo "------------------------------------------------------------" curdir="${PWD}" if [ ${WIPE_WORK_DIR} = 1 ] && [ -d "${WORK_DIR}" ]; then case "${WORK_DIR}" in "."|".."|"/"|${curdir}) \ die "Refusing to 'rm -r WORK_DIR=${WORK_DIR}'";; esac echo "Wiping WORK_DIR='${WORK_DIR}' first." rm -r "${WORK_DIR}" fi if ! [ -d "${WORK_DIR}" ]; then mkdir -p "${WORK_DIR}" || die "Failed mkdir $WORK_DIR" echo "Created WORK_DIR='${WORK_DIR}'." fi cd "${WORK_DIR}" || die "Failed 'cd $WORK_DIR'" echo "Linking hippo files..." setup_hippo || die "Failed to link required files." echo "Copying additional files..." for f in ${INPUTFILES}; do cp "${curdir}/${f}" . || die "Failed copying additional file $f" done echo "Done" </pre> b4bae6168cef642fdb211c12ab859cd44f0b0bcf 12 7 134 85 2008-10-19T15:48:13Z Oliver 2 /* Categories */ Charmm -> Hippo :-) wikitext text/x-wiki This page should tell you how to work with this Wiki &ndash; it's not complicated, promise! (In fact, the whole point of a wiki is to make it as easy for the user as possible to document whatever there is worth documenting). ==Editing an existing page== # Select the ''Edit'' link at the top. # Type or simply copy and paste text, eg from your editor, shell, or an email, and use the ''preview'' button. # Once it looks sort-of right commit your changes by clicking ''save page''. The Media Wiki page has a comprehensive list of the [http://meta.wikipedia.org/wiki/MediaWiki_User%27s_Guide:_Editing_overview#The_wiki_markup Wiki markup] but you can also look at the code of existing pages (edit the page but don't save it) or use the formatting buttons at the top of your editing box. The most important thing is just to put something on the page and not to worry too much about formatting. If in doubt simply leave one initial space and everything gets formatted verbatim; anything resembling an URL will be turned into a link (or enclose it in <nowiki>'[' and ']'</nowiki>). ==Editing a new page== If you click on a red link then you enter a non-existing page. This is not bad: Simply start editing it and ''write it yourself''. You can't make mistakes. Just do it. ==Creating a new page== To make a non-existing page you simply insert the link into an existing page, it appears in red, you click it and then edit it. == Signing your name == Sometimes this is useful: three tildes <nowiki>~~~</nowiki> signs your name like this: [[User:Oliver|Oliver]]; four <nowiki>~~~~</nowiki> dates it too: [[User:Oliver|Oliver]] 18:32, 24 January 2006 (EST) == Categories == [http://meta.wikimedia.org/wiki/Help:Category '''Categories''' in MediaWiki] provide automatic indexes that are useful as tables of contents. See the Special Page '''[[Special:Categories]]''' for a list of all defined categories. * You '''define a category''' by adding one or more special tags at the end of a page: add <tt><nowiki>[[</nowiki>Category:''Category name''<nowiki>]]</nowiki></tt> to the page's wikitext source. For instance, add to page that describes analysis scripts for Charmm <nowiki>[[Category:Hippo]]</nowiki> <nowiki>[[Category:Analysis]]</nowiki> : as the last two lines. This will implicitly define the categories [[:Category:Analysis]] and [[:Category:Hippo]]. * The '''category pages''' can also be edited. In addition, the wiki software adds an alphabetically sorted list of all pages in the category. This makes a category useful as an entry point into a subject. ** One ''must'' edit a category page for the wiki to create the indexed list (even if it is just an empty edit). ** It is also possible to add another category to a category page: This will turn this category in a subcategory on the other category page. * In order to '''reference a category within a page as a normal wiki link''' (without adding the page to the category) prefix the link name with a colon. For example: <tt><nowiki>[[:</nowiki>Category:Analysis<nowiki>]]</nowiki></tt>. == Page maintenance == === Redirection === A 'symbolic link' to another pages is created with the [http://meta.wikimedia.org/wiki/Help:Redirection REDIRECT] command: <nowiki>#REDIRECT [[</nowiki>''page''<nowiki>]]</nowiki> ==Highlighting sourcecode== Wikimedia can do syntax highlighting for over a dozen programming languages, including c, python, perl, fortran, and c++. Just surround the code with a tag of the name of the language. For example: <pre> <python> import re lines = file("ifconf.log").readlines() l_iter = iter(lines) nodes = [] for l in l_iter: if l[:7] == "compute": node = l.split('.')[0] temp = l_iter.next().split() iface, addr = temp[0], temp[4] nodes.append([node, iface, addr]) </python> </pre> Gives you <python> import re lines = file("ifconf.log").readlines() l_iter = iter(lines) nodes = [] for l in l_iter: if l[:7] == "compute": node = l.split('.')[0] temp = l_iter.next().split() iface, addr = temp[0], temp[4] nodes.append([node, iface, addr]) </python> ==Inserting Gnuplot graphs== You can insert gnuplot graphs directly into mediawiki by using the <tt>gnuplot</tt> tag. For example: <pre> <gnuplot> set output 'func_approx.png' plot '-' using 1:2 t 'quadratic approximation' with linesp lt 1 lw 3, \ '-' using 1:2 t 'cubic approximation' with linesp lt 2 lw 3 1 2 2 4 3 8 4 16 e 1 3 2 9 3 27 4 81 e </gnuplot> </pre> Gives you the following: <gnuplot> set output 'func_approx.png' plot '-' using 1:2 t 'quadratic approximation' with linesp lt 1 lw 3, \ '-' using 1:2 t 'cubic approximation' with linesp lt 2 lw 3 1 2 2 4 3 8 4 16 e 1 3 2 9 3 27 4 81 e </gnuplot> == Adding bibliographic references (specifically [http://www.pubmed.gov PubMed]) == You can insert bibliographic references into pages by using the <tt><nowiki><cite></nowiki></tt> and <tt><nowiki><biblio></nowiki></tt> tags. This uses the PubMed id number (pmid) found at the bottom of the abstract listing for a particular article. Mediawiki will go to [http://www.pubmed.gov PubMed] and pull the citation information for the reference. Using the key in front of the pmid assignment within the <tt><nowiki><cite></nowiki></tt> tag (see example below) gives you a reference to the article within the current page. For example, although you can obmit the pmid and simply format the reference yourself. <pre> Recent papers from the Woolf lab <cite>jcp2005 proteins2005 jcp2004</cite>: ===Bibliography=== <biblio> #jcp2005 pmid=15847458 #proteins2005 pmid=15828005 #jcp2004 pmid=15634036 </biblio> </pre> Will give you this: Recent papers from the Woolf lab <cite>jcp2005 proteins2005 jcp2004</cite>: <b>Bibliography</b> <biblio> #jcp2005 pmid=15847458 #proteins2005 pmid=15828005 #jcp2004 pmid=15634036 </biblio> == Images == [[Image:NAChR M2 water.jpg|200px|right]] The following shows two methods of how to incorporate an image in a wiki page. === Upload === The image is uploaded to the webserver and resides in the wiki (somewhere... you don't need to know where, it's a secret) # first [[Special:Upload|upload]] it (use the link in the toolbox on the left) # enter a wiki link such as <tt><nowiki>[[Image:NAChR M2 water.jpg|200px]] </nowiki></tt> into the text An exhaustive description of the image capabilities are discussed in the [http://en.wikipedia.org/wiki/Wikipedia:Extended_image_syntax Wikipedia Extended Image Syntax]. Most importantly, if you want to change the size of the image, add a size option <tt>|''size''px</tt> option (<tt>|200px</tt> in the example above). The new version of MediaWiki gives you a plethora of options to add captions, float the image to left or right, change sizes, show it as a (fast) thumbnail, ... === Web link === Alternatively, just put in a link to a png or jpg such as <tt><nowiki>http://sbcb.bioch.ox.ac.uk/oliver/Priv/USA/California/goldenpoppy.png</nowiki></tt>: http://sbcb.bioch.ox.ac.uk/oliver/Priv/USA/California/goldenpoppy.png The image appears in its original size. == Links == If you want to gain an in-depth knowledge of working with this Wiki then have a look at these links: === Wikipedia edit help documents === * Wikipedia's [http://en.wikipedia.org/wiki/Wikipedia:How_to_edit_a_page full listing of wiki editing commands] (make sure you come back here to edit... otherwise you will be editing Wikipedia) * Wikipedia [http://en.wikipedia.org/wiki/Wikipedia:Extended_image_syntax Extended Image Syntax] for all your image inclusion needs * Syntax of [http://en.wikipedia.org/wiki/Help:Table Table] commands === MediaWiki documents === The [http://wiki.biowerkzeug.org/ Biowerkzeug Wiki] uses the [http://www.mediawiki.org/wiki MediaWiki] software. For more on MediaWiki see the following links: * [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] * [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list] * [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ] * [http://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list] [[Category:Help]] 6b1105f697395c700842fbc9ebcbcb26ef4fa290 135 134 2008-10-19T15:54:50Z Oliver 2 /* Images */ updated images with Hippo ones; weblinking images does not work here wikitext text/x-wiki This page should tell you how to work with this Wiki &ndash; it's not complicated, promise! (In fact, the whole point of a wiki is to make it as easy for the user as possible to document whatever there is worth documenting). ==Editing an existing page== # Select the ''Edit'' link at the top. # Type or simply copy and paste text, eg from your editor, shell, or an email, and use the ''preview'' button. # Once it looks sort-of right commit your changes by clicking ''save page''. The Media Wiki page has a comprehensive list of the [http://meta.wikipedia.org/wiki/MediaWiki_User%27s_Guide:_Editing_overview#The_wiki_markup Wiki markup] but you can also look at the code of existing pages (edit the page but don't save it) or use the formatting buttons at the top of your editing box. The most important thing is just to put something on the page and not to worry too much about formatting. If in doubt simply leave one initial space and everything gets formatted verbatim; anything resembling an URL will be turned into a link (or enclose it in <nowiki>'[' and ']'</nowiki>). ==Editing a new page== If you click on a red link then you enter a non-existing page. This is not bad: Simply start editing it and ''write it yourself''. You can't make mistakes. Just do it. ==Creating a new page== To make a non-existing page you simply insert the link into an existing page, it appears in red, you click it and then edit it. == Signing your name == Sometimes this is useful: three tildes <nowiki>~~~</nowiki> signs your name like this: [[User:Oliver|Oliver]]; four <nowiki>~~~~</nowiki> dates it too: [[User:Oliver|Oliver]] 18:32, 24 January 2006 (EST) == Categories == [http://meta.wikimedia.org/wiki/Help:Category '''Categories''' in MediaWiki] provide automatic indexes that are useful as tables of contents. See the Special Page '''[[Special:Categories]]''' for a list of all defined categories. * You '''define a category''' by adding one or more special tags at the end of a page: add <tt><nowiki>[[</nowiki>Category:''Category name''<nowiki>]]</nowiki></tt> to the page's wikitext source. For instance, add to page that describes analysis scripts for Charmm <nowiki>[[Category:Hippo]]</nowiki> <nowiki>[[Category:Analysis]]</nowiki> : as the last two lines. This will implicitly define the categories [[:Category:Analysis]] and [[:Category:Hippo]]. * The '''category pages''' can also be edited. In addition, the wiki software adds an alphabetically sorted list of all pages in the category. This makes a category useful as an entry point into a subject. ** One ''must'' edit a category page for the wiki to create the indexed list (even if it is just an empty edit). ** It is also possible to add another category to a category page: This will turn this category in a subcategory on the other category page. * In order to '''reference a category within a page as a normal wiki link''' (without adding the page to the category) prefix the link name with a colon. For example: <tt><nowiki>[[:</nowiki>Category:Analysis<nowiki>]]</nowiki></tt>. == Page maintenance == === Redirection === A 'symbolic link' to another pages is created with the [http://meta.wikimedia.org/wiki/Help:Redirection REDIRECT] command: <nowiki>#REDIRECT [[</nowiki>''page''<nowiki>]]</nowiki> ==Highlighting sourcecode== Wikimedia can do syntax highlighting for over a dozen programming languages, including c, python, perl, fortran, and c++. Just surround the code with a tag of the name of the language. For example: <pre> <python> import re lines = file("ifconf.log").readlines() l_iter = iter(lines) nodes = [] for l in l_iter: if l[:7] == "compute": node = l.split('.')[0] temp = l_iter.next().split() iface, addr = temp[0], temp[4] nodes.append([node, iface, addr]) </python> </pre> Gives you <python> import re lines = file("ifconf.log").readlines() l_iter = iter(lines) nodes = [] for l in l_iter: if l[:7] == "compute": node = l.split('.')[0] temp = l_iter.next().split() iface, addr = temp[0], temp[4] nodes.append([node, iface, addr]) </python> ==Inserting Gnuplot graphs== You can insert gnuplot graphs directly into mediawiki by using the <tt>gnuplot</tt> tag. For example: <pre> <gnuplot> set output 'func_approx.png' plot '-' using 1:2 t 'quadratic approximation' with linesp lt 1 lw 3, \ '-' using 1:2 t 'cubic approximation' with linesp lt 2 lw 3 1 2 2 4 3 8 4 16 e 1 3 2 9 3 27 4 81 e </gnuplot> </pre> Gives you the following: <gnuplot> set output 'func_approx.png' plot '-' using 1:2 t 'quadratic approximation' with linesp lt 1 lw 3, \ '-' using 1:2 t 'cubic approximation' with linesp lt 2 lw 3 1 2 2 4 3 8 4 16 e 1 3 2 9 3 27 4 81 e </gnuplot> == Adding bibliographic references (specifically [http://www.pubmed.gov PubMed]) == You can insert bibliographic references into pages by using the <tt><nowiki><cite></nowiki></tt> and <tt><nowiki><biblio></nowiki></tt> tags. This uses the PubMed id number (pmid) found at the bottom of the abstract listing for a particular article. Mediawiki will go to [http://www.pubmed.gov PubMed] and pull the citation information for the reference. Using the key in front of the pmid assignment within the <tt><nowiki><cite></nowiki></tt> tag (see example below) gives you a reference to the article within the current page. For example, although you can obmit the pmid and simply format the reference yourself. <pre> Recent papers from the Woolf lab <cite>jcp2005 proteins2005 jcp2004</cite>: ===Bibliography=== <biblio> #jcp2005 pmid=15847458 #proteins2005 pmid=15828005 #jcp2004 pmid=15634036 </biblio> </pre> Will give you this: Recent papers from the Woolf lab <cite>jcp2005 proteins2005 jcp2004</cite>: <b>Bibliography</b> <biblio> #jcp2005 pmid=15847458 #proteins2005 pmid=15828005 #jcp2004 pmid=15634036 </biblio> == Images == The following shows two methods of how to incorporate an image in a wiki page. === Upload === The image is uploaded to the webserver and resides in the wiki (somewhere... you don't need to know where, it's a secret) # first [[Special:Upload|upload]] it (use the link in the toolbox on the left) # enter a wiki link such as <tt><nowiki>[[Image:Gbim.jpg|200px]] </nowiki></tt> into the text. [[Image:Gbim.jpg|200px]] [[Image:Gbim.jpg|thumb|right|150px|Insertion of a peptide into a Generalized Born implicit membrane.]] An exhaustive description of the image capabilities are discussed in the [http://en.wikipedia.org/wiki/Wikipedia:Extended_image_syntax Wikipedia Extended Image Syntax]. Most importantly, if you want to change the size of the image, add a size option <tt>|''size''px</tt> option (<tt>|200px</tt> in the example above). The new version of MediaWiki gives you a plethora of options to add captions, float the image to left or right, change sizes, show it as a (fast) thumbnail, ... <tt><nowiki>[[Image:Gbim.jpg|thumb|right|150px|Insertion of a peptide into a Generalized Born implicit membrane.]]</nowiki></tt> gives a thumbnail image floating on the right hand side. == Links == If you want to gain an in-depth knowledge of working with this Wiki then have a look at these links: === Wikipedia edit help documents === * Wikipedia's [http://en.wikipedia.org/wiki/Wikipedia:How_to_edit_a_page full listing of wiki editing commands] (make sure you come back here to edit... otherwise you will be editing Wikipedia) * Wikipedia [http://en.wikipedia.org/wiki/Wikipedia:Extended_image_syntax Extended Image Syntax] for all your image inclusion needs * Syntax of [http://en.wikipedia.org/wiki/Help:Table Table] commands === MediaWiki documents === The [http://wiki.biowerkzeug.org/ Biowerkzeug Wiki] uses the [http://www.mediawiki.org/wiki MediaWiki] software. For more on MediaWiki see the following links: * [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] * [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list] * [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ] * [http://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list] [[Category:Help]] 5bedc4eb600a08b71ac67a2481ad6a7aa0e918c7 2 48 137 2008-11-12T15:24:08Z Kaihsu 10 New page: [http://sbcb.bioch.ox.ac.uk/kaihsu/ Kaihsu Tai] wikitext text/x-wiki [http://sbcb.bioch.ox.ac.uk/kaihsu/ Kaihsu Tai] 5408115b390806a8f4ccef08e6c1781c5cde20a0 6 49 138 2008-11-13T13:47:48Z Kaihsu 10 not this hippo wikitext text/x-wiki not this hippo 74209a4c64022d86079ec58f7727be4690764031 139 138 2008-11-13T13:48:41Z Kaihsu 10 wikitext text/x-wiki not this hippo Licensed under GFDL from [http://commons.wikimedia.org/wiki/Image:Nijlpaard.jpg]; see there for details of licence. d9dc44faf239052dfd2d1a55566ac4fe6c991711 0 1 141 98 2008-11-13T13:50:13Z Kaihsu 10 /* Hippo */ wikitext text/x-wiki <div id="hauptseite"> {| width="100%" cellspacing="0" cellpadding="0" | colspan="2" | This Wiki discusses biomolecular simulations with '''[[Hippo]]''' and other molecular dynamics/Monte Carlo codes. It serves as a repository for the community and complements the [http://forums.biowerkzeug.org forums]. Please contribute your own knowledge to this Wiki: If anything is unclear and you know how to write it better – change it. If you have useful tips & tricks – share them with everyone else. If you have comments on any article in this Wiki – start a discussion on the ''discussion'' page that accompanies every article (look in the top menu bar). We only ask you to [[Special:Userlogin|register]] when you edit pages. See [[Help:Editing|Help&rarr;Editing]] to get started on contributing to this community resource. Follow the links below, use the search on the left, or browse articles by [[Special:Categories|category]]. |- | width="50%" style="vertical-align:top;" | <div id="Hippo" class="hauptseite-links"> == Hippo == <div class="inhalt"> [[Image:Hippopotamus.jpg|thumb|right|Not this hippo.]] * [[Hippo|Features]] * [[Simulations]] * [[Analysis]] * [[Graphical interface]] * [[Files]] </div> </div> <div id="Methods" class="hauptseite-links"> == Methods == <div class="inhalt"> * [[Molecular dynamics]] * [[Monte Carlo]] * [[Force fields]] * [[Algorithms]] * [[Solvents]] * [[Membranes]] </div> </div> | width="50%" style="vertical-align:top;" | <div id="Simulation protocols" class="hauptseite-rechts"> == Simulation protocols == <div class="inhalt"> * [[Globular proteins]] in solvent * [[Membrane proteins]] in membrane and solvent * [[Free energy calculations]] * [[Transition path sampling]] </div> </div> <div id="Visualization" class="hauptseite-rechts"> == Visualization == <div class="inhalt"> * [[Visualization software|Software]] * [[Visualization tutorial|tutorial]] with [[VMD]] * [[Movie tutorial]] </div> </div> <div id="Software" class="hauptseite-rechts"> == Software == <div class="inhalt"> * [[Molecular dynamics codes]] * [[Monte Carlo codes]] * [[Electrostatics]] and [[Brownian dynamics]] * [[Model building]] * [[Visualization software|Visualization]] * [[Analysis software]] </div> </div> |} </div> __NOTOC__ de88f2551d14b847b478c2996701d8b819418e71 142 141 2008-11-14T11:52:10Z Oliver 2 /* Hippo */ wikitext text/x-wiki <div id="hauptseite"> {| width="100%" cellspacing="0" cellpadding="0" | colspan="2" | This Wiki discusses biomolecular simulations with '''[[Hippo]]''' and other molecular dynamics/Monte Carlo codes. It serves as a repository for the community and complements the [http://forums.biowerkzeug.org forums]. Please contribute your own knowledge to this Wiki: If anything is unclear and you know how to write it better – change it. If you have useful tips & tricks – share them with everyone else. If you have comments on any article in this Wiki – start a discussion on the ''discussion'' page that accompanies every article (look in the top menu bar). We only ask you to [[Special:Userlogin|register]] when you edit pages. See [[Help:Editing|Help&rarr;Editing]] to get started on contributing to this community resource. Follow the links below, use the search on the left, or browse articles by [[Special:Categories|category]]. |- | width="50%" style="vertical-align:top;" | <div id="Hippo" class="hauptseite-links"> == Hippo == <div class="inhalt"> [[Image:Hippopotamus.jpg|thumb|right|Not this hippo.]] * [[Hippo|Features]] * [[Simulations]] * [[Analysis]] * [[Graphical interface]] * [[Files]] * [[Benchmarks]] </div> </div> <div id="Methods" class="hauptseite-links"> == Methods == <div class="inhalt"> * [[Molecular dynamics]] * [[Monte Carlo]] * [[Force fields]] * [[Algorithms]] * [[Solvents]] * [[Membranes]] </div> </div> | width="50%" style="vertical-align:top;" | <div id="Simulation protocols" class="hauptseite-rechts"> == Simulation protocols == <div class="inhalt"> * [[Globular proteins]] in solvent * [[Membrane proteins]] in membrane and solvent * [[Free energy calculations]] * [[Transition path sampling]] </div> </div> <div id="Visualization" class="hauptseite-rechts"> == Visualization == <div class="inhalt"> * [[Visualization software|Software]] * [[Visualization tutorial|tutorial]] with [[VMD]] * [[Movie tutorial]] </div> </div> <div id="Software" class="hauptseite-rechts"> == Software == <div class="inhalt"> * [[Molecular dynamics codes]] * [[Monte Carlo codes]] * [[Electrostatics]] and [[Brownian dynamics]] * [[Model building]] * [[Visualization software|Visualization]] * [[Analysis software]] </div> </div> |} </div> __NOTOC__ 1173ada4101ff169b92155c1cfaf44d09435c9a8 143 142 2008-11-14T11:52:40Z Oliver 2 /* Hippo */ wikitext text/x-wiki <div id="hauptseite"> {| width="100%" cellspacing="0" cellpadding="0" | colspan="2" | This Wiki discusses biomolecular simulations with '''[[Hippo]]''' and other molecular dynamics/Monte Carlo codes. It serves as a repository for the community and complements the [http://forums.biowerkzeug.org forums]. Please contribute your own knowledge to this Wiki: If anything is unclear and you know how to write it better – change it. If you have useful tips & tricks – share them with everyone else. If you have comments on any article in this Wiki – start a discussion on the ''discussion'' page that accompanies every article (look in the top menu bar). We only ask you to [[Special:Userlogin|register]] when you edit pages. See [[Help:Editing|Help&rarr;Editing]] to get started on contributing to this community resource. Follow the links below, use the search on the left, or browse articles by [[Special:Categories|category]]. |- | width="50%" style="vertical-align:top;" | <div id="Hippo" class="hauptseite-links"> == Hippo == <div class="inhalt"> [[Image:Hippopotamus.jpg|thumb|right|Not this hippo.]] * [[Hippo|Features]] * [[Simulations]] * [[Analysis]] * [[Graphical interface]] * [[Files]] * [[Performance]] </div> </div> <div id="Methods" class="hauptseite-links"> == Methods == <div class="inhalt"> * [[Molecular dynamics]] * [[Monte Carlo]] * [[Force fields]] * [[Algorithms]] * [[Solvents]] * [[Membranes]] </div> </div> | width="50%" style="vertical-align:top;" | <div id="Simulation protocols" class="hauptseite-rechts"> == Simulation protocols == <div class="inhalt"> * [[Globular proteins]] in solvent * [[Membrane proteins]] in membrane and solvent * [[Free energy calculations]] * [[Transition path sampling]] </div> </div> <div id="Visualization" class="hauptseite-rechts"> == Visualization == <div class="inhalt"> * [[Visualization software|Software]] * [[Visualization tutorial|tutorial]] with [[VMD]] * [[Movie tutorial]] </div> </div> <div id="Software" class="hauptseite-rechts"> == Software == <div class="inhalt"> * [[Molecular dynamics codes]] * [[Monte Carlo codes]] * [[Electrostatics]] and [[Brownian dynamics]] * [[Model building]] * [[Visualization software|Visualization]] * [[Analysis software]] </div> </div> |} </div> __NOTOC__ 675555f9099f33d90c0ff89711e329210f07f529 0 50 144 2008-11-14T12:13:54Z Oliver 2 performance benchmark, PLEASE ADD YOUR OWN wikitext text/x-wiki As a basic performance test we run the simulations in the <tt>test</tt> directory with these commands (on Linux): cd testjobs time ./calc_testjobs We report the ''user'' time. CPU properties are found with cat /proc/cpuinfo Note that these tests only utilize a single core. Also report the binary used (<tt>hippo</tt> or <tt>hippo_p3</tt> and the revision). Please feel free to add your own results. {| class="wikitable" |- ! CPU make ! model ! GHz ! cores ! time ! binary ! rev |- | Intel Xeon Quad | L5410 | 2.33 | 4 | 1:27 min | hippo | beta rev32 |- | Intel Core Duo | T2300 | 1.66 | 2 | 2:41 min | hippo_p3 | beta rev32 |} dcde5cacc48a7a1fcb345d5bcf6186db87db96d5 145 144 2008-11-14T12:22:07Z Oliver 2 added old AMD XP wikitext text/x-wiki As a basic performance test we run the simulations in the <tt>test</tt> directory with these commands (on Linux): cd testjobs time ./calc_testjobs We report the ''user'' time. CPU properties are found with cat /proc/cpuinfo Note that these tests only utilize a single core. Also report the binary used (<tt>hippo</tt> or <tt>hippo_p3</tt> and the revision). Please feel free to add your own results. {| class="wikitable" |- ! CPU make ! model ! GHz ! cores ! time/min ! binary ! rev |- | Intel Xeon Quad | L5410 | 2.33 | 4 | 1:27 | hippo | beta rev32 |- | Intel Core Duo | T2300 (Mac Mini) | 1.66 | 2 | 2:41 | hippo_p3 | beta rev32 |- | [http://en.wikipedia.org/wiki/List_of_AMD_Athlon_XP_microprocessors#Athlon_XP_.22Palomino.22_.28Model_6.2C_180_nm.29 AMD Athlon XP 1800+] | AX1800DMT3C | 1.533 ? | 1 | 4:30 | hippo_p3 | beta rev26 |} f1f71fa79a0657e29ce70e253a2021da43737364 146 145 2008-11-14T12:22:26Z Oliver 2 wikitext text/x-wiki As a basic performance test we run the simulations in the <tt>test</tt> directory with these commands (on Linux): cd testjobs time ./calc_testjobs We report the ''user'' time. CPU properties are found with cat /proc/cpuinfo Note that these tests only utilize a single core. Also report the binary used (<tt>hippo</tt> or <tt>hippo_p3</tt> and the revision). Please feel free to add your own results. {| class="wikitable" |- ! CPU make ! model ! GHz ! cores ! time/min ! binary ! rev |- | Intel Xeon Quad | L5410 | 2.33 | 4 | 1:27 | hippo | beta rev32 |- | Intel Core Duo | T2300 (Mac Mini) | 1.66 | 2 | 2:41 | hippo_p3 | beta rev32 |- | [http://en.wikipedia.org/wiki/List_of_AMD_Athlon_XP_microprocessors#Athlon_XP_.22Palomino.22_.28Model_6.2C_180_nm.29 AMD Athlon XP 1800+] | AX1800DMT3C | 1.53 | 1 | 4:30 | hippo_p3 | beta rev26 |} 87c88e1dd46a9eb80852142ea73ec38e24c58e28 147 146 2008-11-14T14:27:06Z Oliver 2 hippo_p3 on Q wikitext text/x-wiki As a basic performance test we run the simulations in the <tt>test</tt> directory with these commands (on Linux): cd testjobs time ./calc_testjobs We report the ''user'' time. CPU properties are found with cat /proc/cpuinfo Note that these tests only utilize a single core. Also report the binary used (<tt>hippo</tt> or <tt>hippo_p3</tt> and the revision). Please feel free to add your own results. {| class="wikitable" |- ! CPU make ! model ! GHz ! cores ! time/min ! binary ! rev |- | Intel Xeon Quad | L5410 | 2.33 | 4 | 1:27 | hippo | beta rev32 |- | Intel Xeon Quad | L5410 | 2.33 | 4 | 1:31 | hippo_p3 | beta rev32 |- | Intel Core Duo | T2300 (Mac Mini) | 1.66 | 2 | 2:41 | hippo_p3 | beta rev32 |- | [http://en.wikipedia.org/wiki/List_of_AMD_Athlon_XP_microprocessors#Athlon_XP_.22Palomino.22_.28Model_6.2C_180_nm.29 AMD Athlon XP 1800+] | AX1800DMT3C | 1.53 | 1 | 4:30 | hippo_p3 | beta rev26 |} 402fba3d08fd4e9d95b0b6be9e348289d96b78be 148 147 2008-11-14T14:49:27Z Oliver 2 links to model names; reformatted table wikitext text/x-wiki As a basic performance test we run the simulations in the <tt>test</tt> directory with these commands (on Linux): cd testjobs time ./calc_testjobs We report the ''user'' time. CPU properties are found with cat /proc/cpuinfo and model names from [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors List_of_Intel_microprocessors] for Intel (also see the [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors#Detailed_x86_architecture_microprocessor_lists detailed lists of Intel x86 cpus]) and [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors List_of_AMD_microprocessors] for AMD cpus (also see the [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors#Detailed_microprocessor_release_lists detailed lists of AMD cpus]. Also report the binary used (<tt>hippo</tt> or <tt>hippo_p3</tt>) and the revision. Note that these tests only utilize a ''single core''. Please add your own results. {| class="wikitable" |- ! Vendor ! model ! GHz ! cores ! time/min ! binary ! revision |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410] | 2.33 | 4 | 1:27 | hippo | rev32 |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410] | 2.33 | 4 | 1:31 | hippo_p3 | rev32 |- | Intel | Core Duo T2300 (Mac Mini) | 1.66 | 2 | 2:41 | hippo_p3 | rev32 |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Athlon_XP_microprocessors#Athlon_XP_.22Palomino.22_.28Model_6.2C_180_nm.29 Athlon XP 1800+] | 1.53 | 1 | 4:30 | hippo_p3 | rev26 |} c4ee770b91e3ee99a6de170bb1c893176841c279 149 148 2008-11-14T14:54:51Z Oliver 2 wikitext text/x-wiki As a basic performance test we run the simulations in the <tt>test</tt> directory with these commands (on Linux): cd testjobs time ./calc_testjobs We report the ''user'' time. CPU properties are found with cat /proc/cpuinfo and model names from [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors List_of_Intel_microprocessors] for Intel (also see the [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors#Detailed_x86_architecture_microprocessor_lists detailed lists of Intel x86 cpus]) and [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors List_of_AMD_microprocessors] for AMD cpus (also see the [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors#Detailed_microprocessor_release_lists detailed lists of AMD cpus]. Also report the binary used (<tt>hippo</tt> or <tt>hippo_p3</tt>) and the revision. Note that these tests only utilize a ''single core''. Please add your own results. {| class="wikitable" |- ! vendor ! model ! GHz ! cores ! time/min ! binary ! revision |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410] | 2.33 | 4 | 1:27 | hippo | rev32 |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410] | 2.33 | 4 | 1:31 | hippo_p3 | rev32 |- | Intel | Core Duo T2300 (Mac Mini) | 1.66 | 2 | 2:41 | hippo_p3 | rev32 |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Athlon_XP_microprocessors#Athlon_XP_.22Palomino.22_.28Model_6.2C_180_nm.29 Athlon XP 1800+] | 1.53 | 1 | 4:30 | hippo_p3 | rev26 |} 8d0249afd41a018c86437badfd7c4e2e7f93530c 150 149 2008-11-14T14:58:38Z Kaihsu 10 wikitext text/x-wiki As a basic performance test we run the simulations in the <tt>test</tt> directory with these commands (on Linux): cd testjobs time ./calc_testjobs We report the ''user'' time. CPU properties are found with cat /proc/cpuinfo and model names from [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors List_of_Intel_microprocessors] for Intel (also see the [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors#Detailed_x86_architecture_microprocessor_lists detailed lists of Intel x86 cpus]) and [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors List_of_AMD_microprocessors] for AMD cpus (also see the [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors#Detailed_microprocessor_release_lists detailed lists of AMD cpus]. Also report the binary used (<tt>hippo</tt> or <tt>hippo_p3</tt>) and the revision. Note that these tests only utilize a ''single core''. Please add your own results. {| class="wikitable" |- ! vendor ! model ! GHz ! cores ! time/min ! binary ! revision |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410] | 2.33 | 4 | 1:27 | hippo | rev32 |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410] | 2.33 | 4 | 1:31 | hippo_p3 | rev32 <!-- tinman --> |- | Intel | Core Duo T2300 (Mac Mini) | 1.66 | 2 | 2:41 | hippo_p3 | rev32 <!-- abbondanza --> |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Athlon_XP_microprocessors#Athlon_XP_.22Palomino.22_.28Model_6.2C_180_nm.29 Athlon XP 1800+] | 1.53 | 1 | 4:30 | hippo_p3 | rev26 |} 096ff26a203dc99bb9c0797c1011873431bf00ae 0 50 151 150 2008-11-14T15:09:57Z Oliver 2 Xeon 2.4 wikitext text/x-wiki As a basic performance test we run the simulations in the <tt>test</tt> directory with these commands (on Linux): cd testjobs time ./calc_testjobs We report the ''user'' time. CPU properties are found with cat /proc/cpuinfo and model names from [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors List_of_Intel_microprocessors] for Intel (also see the [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors#Detailed_x86_architecture_microprocessor_lists detailed lists of Intel x86 cpus]) and [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors List_of_AMD_microprocessors] for AMD cpus (also see the [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors#Detailed_microprocessor_release_lists detailed lists of AMD cpus]. Also report the binary used (<tt>hippo</tt> or <tt>hippo_p3</tt>) and the revision. Note that these tests only utilize a ''single core''. Please add your own results. {| class="wikitable" |- ! vendor ! model ! GHz ! cores ! time/min ! binary ! revision |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410] | 2.33 | 4 | 1:27 | hippo | rev32 |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410] | 2.33 | 4 | 1:31 | hippo_p3 | rev32 <!-- tinman --> |- | Intel | Core Duo T2300 (Mac Mini) | 1.66 | 2 | 2:41 | hippo_p3 | rev32 <!-- abbondanza --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Prestonia.22_.28standard-voltage.2C_130_nm.29 Xeon 2.4] | 2.4 | 1 | 3:03 | hippo_p3 | rev26 <!-- timberwulf --> |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Athlon_XP_microprocessors#Athlon_XP_.22Palomino.22_.28Model_6.2C_180_nm.29 Athlon XP 1800+] | 1.53 | 1 | 4:30 | hippo_p3 | rev26 |} 66042c41f675fa249ec0eadb76b64887e38a6623 152 151 2008-11-14T15:11:08Z Oliver 2 wikitext text/x-wiki As a basic performance test we run the simulations in the <tt>test</tt> directory with these commands (on Linux): cd testjobs time ./calc_testjobs We report the ''user'' time. CPU properties are found with cat /proc/cpuinfo and model names from [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors List_of_Intel_microprocessors] for Intel (also see the [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors#Detailed_x86_architecture_microprocessor_lists detailed lists of Intel x86 cpus]) and [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors List_of_AMD_microprocessors] for AMD cpus (also see the [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors#Detailed_microprocessor_release_lists detailed lists of AMD cpus]). Also report the binary used (<tt>hippo</tt> or <tt>hippo_p3</tt>) and the revision. Note that these tests only utilize a ''single core''. Please add your own results. {| class="wikitable" |- ! vendor ! model ! GHz ! cores ! time/min ! binary ! revision |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410] | 2.33 | 4 | 1:27 | hippo | rev32 |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410] | 2.33 | 4 | 1:31 | hippo_p3 | rev32 <!-- tinman --> |- | Intel | Core Duo T2300 (Mac Mini) | 1.66 | 2 | 2:41 | hippo_p3 | rev32 <!-- abbondanza --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Prestonia.22_.28standard-voltage.2C_130_nm.29 Xeon 2.4] | 2.4 | 1 | 3:03 | hippo_p3 | rev26 <!-- timberwulf --> |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Athlon_XP_microprocessors#Athlon_XP_.22Palomino.22_.28Model_6.2C_180_nm.29 Athlon XP 1800+] | 1.53 | 1 | 4:30 | hippo_p3 | rev26 |} aa392e99e4149e317a0b991be699a38dd52d521e 153 152 2008-11-14T15:57:52Z Oliver 2 reformatting + caveat + awk script to parse cpuinfo wikitext text/x-wiki As a basic performance test we run the simulations in the <tt>test</tt> directory with these commands (on Linux): cd testjobs time ./calc_testjobs <ul> <li>We report the ''user'' time.</li> <li>CPU properties are found with <pre>cat /proc/cpuinfo</pre> and model names from [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors List_of_Intel_microprocessors] for Intel (also see the [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors#Detailed_x86_architecture_microprocessor_lists detailed lists of Intel x86 cpus]) and [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors List_of_AMD_microprocessors] for AMD cpus (also see the [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors#Detailed_microprocessor_release_lists detailed lists of AMD cpus]).</li> <li>Also report the binary used (<tt>hippo</tt> or <tt>hippo_p3</tt>) and the revision.</li> <li>Note that these tests only utilize a ''single core''.</li> <li>These results only give a rough idea of the ''relative'' performance of different architectures.</li> </ul> Please add your own results. {| class="wikitable" |- ! vendor ! model ! GHz ! cores ! time/min ! binary ! revision |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410] | 2.33 | 4 | 1:27 | hippo | rev32 |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410] | 2.33 | 4 | 1:31 | hippo_p3 | rev32 <!-- tinman --> |- | Intel | Core Duo T2300 (Mac Mini) | 1.66 | 2 | 2:41 | hippo_p3 | rev32 <!-- abbondanza --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Prestonia.22_.28standard-voltage.2C_130_nm.29 Xeon 2.4] | 2.4 | 1 | 3:03 | hippo_p3 | rev26 <!-- timberwulf --> |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Athlon_XP_microprocessors#Athlon_XP_.22Palomino.22_.28Model_6.2C_180_nm.29 Athlon XP 1800+] | 1.53 | 1 | 4:30 | hippo_p3 | rev26 |} <small>(You don't ''have'' to link to the CPU wikipedia page; just put down whatever you got and even if you're unsure. If in doubt just put the output from cat /proc/cpuinfo | \ awk 'BEGIN {FS=":"}; \ /vendor_id/ {vendor=$2}; \ /model name/ {model=$2}; \ /cpu MHz/ {GHz=$2/1000}; \ /siblings/ {cores=$2}; \ END {printf("|-\n| %s\n| %s\n| %.1f\n| %d\n| TIME\n| hippo\n| ?\n", vendor, model, GHz, cores)} into the wiki table and replace ''TIME'' by what you measured.</small> d271f258e01ae2dc102ffb66ee6282f69d862dec 154 153 2008-11-14T15:58:45Z Oliver 2 wikitext text/x-wiki As a basic performance test we run the simulations in the <tt>test</tt> directory with these commands (on Linux): cd testjobs time ./calc_testjobs <ul> <li>We report the ''user'' time.</li> <li>CPU properties are found with <pre>cat /proc/cpuinfo</pre> and model names from [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors List_of_Intel_microprocessors] for Intel (also see the [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors#Detailed_x86_architecture_microprocessor_lists detailed lists of Intel x86 cpus]) and [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors List_of_AMD_microprocessors] for AMD cpus (also see the [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors#Detailed_microprocessor_release_lists detailed lists of AMD cpus]).</li> <li>Also report the binary used (<tt>hippo</tt> or <tt>hippo_p3</tt>) and the revision.</li> <li>Note that these tests only utilize a ''single core''.</li> <li>These results only give a rough idea of the ''relative'' performance of different architectures.</li> </ul> Please add your own results. {| class="wikitable" |- ! vendor ! model ! GHz ! cores ! time/min ! binary ! revision |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410] | 2.33 | 4 | 1:27 | hippo | rev32 |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410] | 2.33 | 4 | 1:31 | hippo_p3 | rev32 <!-- tinman --> |- | Intel | Core Duo T2300 (Mac Mini) | 1.66 | 2 | 2:41 | hippo_p3 | rev32 <!-- abbondanza --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Prestonia.22_.28standard-voltage.2C_130_nm.29 Xeon 2.4] | 2.4 | 1 | 3:03 | hippo_p3 | rev26 <!-- timberwulf --> |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Athlon_XP_microprocessors#Athlon_XP_.22Palomino.22_.28Model_6.2C_180_nm.29 Athlon XP 1800+] | 1.53 | 1 | 4:30 | hippo_p3 | rev26 |} <small>(You don't ''have'' to link to the CPU wikipedia page; just put down whatever you got and even if you're unsure. If in doubt just put the output from cat /proc/cpuinfo | \ awk 'BEGIN {FS=":"}; \ /vendor_id/ {vendor=$2}; \ /model name/ {model=$2}; \ /cpu MHz/ {GHz=$2/1000}; \ /siblings/ {cores=$2}; \ END {printf("|-\n| %s\n| %s\n| %.1f\n| %d\n| TIME\n| ?\n| ?\n", vendor, model, GHz, cores)} into the wiki table and replace ''TIME'' by what you measured.</small> 41c48615ccfde87a48c18d0f0dacc434efc9d2e2 159 154 2008-11-14T19:42:23Z Oliver 2 fixed awk wikitext text/x-wiki As a basic performance test we run the simulations in the <tt>test</tt> directory with these commands (on Linux): cd testjobs time ./calc_testjobs <ul> <li>We report the ''user'' time.</li> <li>CPU properties are found with <pre>cat /proc/cpuinfo</pre> and model names from [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors List_of_Intel_microprocessors] for Intel (also see the [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors#Detailed_x86_architecture_microprocessor_lists detailed lists of Intel x86 cpus]) and [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors List_of_AMD_microprocessors] for AMD cpus (also see the [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors#Detailed_microprocessor_release_lists detailed lists of AMD cpus]).</li> <li>Also report the binary used (<tt>hippo</tt> or <tt>hippo_p3</tt>) and the revision.</li> <li>Note that these tests only utilize a ''single core''.</li> <li>These results only give a rough idea of the ''relative'' performance of different architectures.</li> </ul> Please add your own results. {| class="wikitable" |- ! vendor ! model ! GHz ! cores ! time/min ! binary ! revision |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410] | 2.33 | 4 | 1:27 | hippo | rev32 |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410] | 2.33 | 4 | 1:31 | hippo_p3 | rev32 <!-- tinman --> |- | Intel | Core Duo T2300 (Mac Mini) | 1.66 | 2 | 2:41 | hippo_p3 | rev32 <!-- abbondanza --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Prestonia.22_.28standard-voltage.2C_130_nm.29 Xeon 2.4] | 2.4 | 1 | 3:03 | hippo_p3 | rev26 <!-- timberwulf --> |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Athlon_XP_microprocessors#Athlon_XP_.22Palomino.22_.28Model_6.2C_180_nm.29 Athlon XP 1800+] | 1.53 | 1 | 4:30 | hippo_p3 | rev26 |} <small>(You don't ''have'' to link to the CPU wikipedia page; just put down whatever you got and even if you're unsure. If in doubt just put the output from cat /proc/cpuinfo | \ awk 'BEGIN {FS=":"}; \ /vendor_id/ {vendor=$2}; \ /model name/ {model=$2}; \ /cpu MHz/ {GHz=$2/1000}; \ /siblings/ {cores=$2}; \ END {printf("|-\n| %s\n| %s\n| %.1f\n| %d\n| TIME\n| ?\n| ?\n", vendor, model, GHz, cores)}' into the wiki table and replace ''TIME'' by what you measured.</small> 6849c90ca30876ad7b98a9e35b8a7377f56d7394 160 159 2008-11-14T19:48:49Z Oliver 2 deathspud results wikitext text/x-wiki As a basic performance test we run the simulations in the <tt>test</tt> directory with these commands (on Linux): cd testjobs time ./calc_testjobs <ul> <li>We report the ''user'' time.</li> <li>CPU properties are found with <pre>cat /proc/cpuinfo</pre> and model names from [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors List_of_Intel_microprocessors] for Intel (also see the [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors#Detailed_x86_architecture_microprocessor_lists detailed lists of Intel x86 cpus]) and [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors List_of_AMD_microprocessors] for AMD cpus (also see the [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors#Detailed_microprocessor_release_lists detailed lists of AMD cpus]).</li> <li>Also report the binary used (<tt>hippo</tt> or <tt>hippo_p3</tt>) and the revision.</li> <li>Note that these tests only utilize a ''single core''.</li> <li>These results only give a rough idea of the ''relative'' performance of different architectures.</li> </ul> Please add your own results. {| class="wikitable" |- ! vendor ! model ! GHz ! cores ! time/min ! binary ! revision |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Core_2_microprocessors#.22Yorkfield.22_.2845_nm.29 Core 2 Quad Q9550] | 2.83 | 4 | 1:04 | hippo | rev32 <!-- deathspud --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410] | 2.33 | 4 | 1:27 | hippo | rev32 |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410] | 2.33 | 4 | 1:31 | hippo_p3 | rev32 <!-- tinman --> |- | Intel | Core Duo T2300 (Mac Mini) | 1.66 | 2 | 2:41 | hippo_p3 | rev32 <!-- abbondanza --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Prestonia.22_.28standard-voltage.2C_130_nm.29 Xeon 2.4] | 2.4 | 1 | 3:03 | hippo_p3 | rev26 <!-- timberwulf --> |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Athlon_XP_microprocessors#Athlon_XP_.22Palomino.22_.28Model_6.2C_180_nm.29 Athlon XP 1800+] | 1.53 | 1 | 4:30 | hippo_p3 | rev26 |} <small>(You don't ''have'' to link to the CPU wikipedia page; just put down whatever you got and even if you're unsure. If in doubt just put the output from cat /proc/cpuinfo | \ awk 'BEGIN {FS=":"}; \ /vendor_id/ {vendor=$2}; \ /model name/ {model=$2}; \ /cpu MHz/ {GHz=$2/1000}; \ /siblings/ {cores=$2}; \ END {printf("|-\n| %s\n| %s\n| %.1f\n| %d\n| TIME\n| ?\n| ?\n", vendor, model, GHz, cores)}' into the wiki table and replace ''TIME'' by what you measured.</small> 23536f24bf8f71915a9236d8aed8b5691d116b38 161 160 2008-11-14T19:52:57Z Oliver 2 deathspud p3 wikitext text/x-wiki As a basic performance test we run the simulations in the <tt>test</tt> directory with these commands (on Linux): cd testjobs time ./calc_testjobs <ul> <li>We report the ''user'' time.</li> <li>CPU properties are found with <pre>cat /proc/cpuinfo</pre> and model names from [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors List_of_Intel_microprocessors] for Intel (also see the [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors#Detailed_x86_architecture_microprocessor_lists detailed lists of Intel x86 cpus]) and [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors List_of_AMD_microprocessors] for AMD cpus (also see the [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors#Detailed_microprocessor_release_lists detailed lists of AMD cpus]).</li> <li>Also report the binary used (<tt>hippo</tt> or <tt>hippo_p3</tt>) and the revision.</li> <li>Note that these tests only utilize a ''single core''.</li> <li>These results only give a rough idea of the ''relative'' performance of different architectures.</li> </ul> Please add your own results. {| class="wikitable" |- ! vendor ! model ! GHz ! cores ! time/min ! binary ! revision |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Core_2_microprocessors#.22Yorkfield.22_.2845_nm.29 Core 2 Quad Q9550] | 2.83 | 4 | 1:04 | hippo | rev32 <!-- deathspud --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Core_2_microprocessors#.22Yorkfield.22_.2845_nm.29 Core 2 Quad Q9550] | 2.83 | 4 | 1:06 | hippo_p3 | rev32 <!-- deathspud --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410] | 2.33 | 4 | 1:27 | hippo | rev32 |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410] | 2.33 | 4 | 1:31 | hippo_p3 | rev32 <!-- tinman --> |- | Intel | Core Duo T2300 (Mac Mini) | 1.66 | 2 | 2:41 | hippo_p3 | rev32 <!-- abbondanza --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Prestonia.22_.28standard-voltage.2C_130_nm.29 Xeon 2.4] | 2.4 | 1 | 3:03 | hippo_p3 | rev26 <!-- timberwulf --> |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Athlon_XP_microprocessors#Athlon_XP_.22Palomino.22_.28Model_6.2C_180_nm.29 Athlon XP 1800+] | 1.53 | 1 | 4:30 | hippo_p3 | rev26 |} <small>(You don't ''have'' to link to the CPU wikipedia page; just put down whatever you got and even if you're unsure. If in doubt just put the output from cat /proc/cpuinfo | \ awk 'BEGIN {FS=":"}; \ /vendor_id/ {vendor=$2}; \ /model name/ {model=$2}; \ /cpu MHz/ {GHz=$2/1000}; \ /siblings/ {cores=$2}; \ END {printf("|-\n| %s\n| %s\n| %.1f\n| %d\n| TIME\n| ?\n| ?\n", vendor, model, GHz, cores)}' into the wiki table and replace ''TIME'' by what you measured.</small> 9dd1c9754e0b2c29e4dc91828562e4acbc080323 162 161 2008-11-14T20:00:25Z Oliver 2 gltph Opteron wikitext text/x-wiki As a basic performance test we run the simulations in the <tt>test</tt> directory with these commands (on Linux): cd testjobs time ./calc_testjobs <ul> <li>We report the ''user'' time.</li> <li>CPU properties are found with <pre>cat /proc/cpuinfo</pre> and model names from [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors List_of_Intel_microprocessors] for Intel (also see the [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors#Detailed_x86_architecture_microprocessor_lists detailed lists of Intel x86 cpus]) and [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors List_of_AMD_microprocessors] for AMD cpus (also see the [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors#Detailed_microprocessor_release_lists detailed lists of AMD cpus]).</li> <li>Also report the binary used (<tt>hippo</tt> or <tt>hippo_p3</tt>) and the revision.</li> <li>Note that these tests only utilize a ''single core''.</li> <li>These results only give a rough idea of the ''relative'' performance of different architectures.</li> </ul> Please add your own results. {| class="wikitable" |- ! vendor ! model ! GHz ! cores ! time/min ! binary ! revision |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Core_2_microprocessors#.22Yorkfield.22_.2845_nm.29 Core 2 Quad Q9550] | 2.83 | 4 | 1:04 | hippo | rev32 <!-- deathspud --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Core_2_microprocessors#.22Yorkfield.22_.2845_nm.29 Core 2 Quad Q9550] | 2.83 | 4 | 1:06 | hippo_p3 | rev32 <!-- deathspud --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410] | 2.33 | 4 | 1:27 | hippo | rev32 |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410] | 2.33 | 4 | 1:31 | hippo_p3 | rev32 <!-- tinman --> |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Opteron_microprocessors#Opteron_200-series_.22SledgeHammer.22_.28B3_.26_C0_.26_CG.2C_130_nm.29 Opteron 248] | 2.2 | 1 | 2:18 | hippo_p3 | rev32 <!-- gltph --> |- | Intel | Core Duo T2300 (Mac Mini) | 1.66 | 2 | 2:41 | hippo_p3 | rev32 <!-- abbondanza --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Prestonia.22_.28standard-voltage.2C_130_nm.29 Xeon 2.4] | 2.4 | 1 | 3:03 | hippo_p3 | rev26 <!-- timberwulf --> |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Athlon_XP_microprocessors#Athlon_XP_.22Palomino.22_.28Model_6.2C_180_nm.29 Athlon XP 1800+] | 1.53 | 1 | 4:30 | hippo_p3 | rev26 |} <small>(You don't ''have'' to link to the CPU wikipedia page; just put down whatever you got and even if you're unsure. If in doubt just put the output from cat /proc/cpuinfo | \ awk 'BEGIN {FS=":"}; \ /vendor_id/ {vendor=$2}; \ /model name/ {model=$2}; \ /cpu MHz/ {GHz=$2/1000}; \ /siblings/ {cores=$2}; \ END {printf("|-\n| %s\n| %s\n| %.1f\n| %d\n| TIME\n| ?\n| ?\n", vendor, model, GHz, cores)}' into the wiki table and replace ''TIME'' by what you measured.</small> f2705955fc2b9507a95268663c71dac76aeabf06 166 162 2008-11-21T01:27:02Z Oliver 2 Phenom wikitext text/x-wiki As a basic performance test we run the simulations in the <tt>test</tt> directory with these commands (on Linux): cd testjobs time ./calc_testjobs <ul> <li>We report the ''user'' time.</li> <li>CPU properties are found with <pre>cat /proc/cpuinfo</pre> and model names from [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors List_of_Intel_microprocessors] for Intel (also see the [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors#Detailed_x86_architecture_microprocessor_lists detailed lists of Intel x86 cpus]) and [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors List_of_AMD_microprocessors] for AMD cpus (also see the [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors#Detailed_microprocessor_release_lists detailed lists of AMD cpus]).</li> <li>Also report the binary used (<tt>hippo</tt> or <tt>hippo_p3</tt>) and the revision.</li> <li>Note that these tests only utilize a ''single core''.</li> <li>These results only give a rough idea of the ''relative'' performance of different architectures.</li> </ul> Please add your own results. {| class="wikitable" |- ! vendor ! model ! GHz ! cores ! time/min ! binary ! revision |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Core_2_microprocessors#.22Yorkfield.22_.2845_nm.29 Core 2 Quad Q9550] | 2.83 | 4 | 1:04 | hippo | rev32 <!-- deathspud --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Core_2_microprocessors#.22Yorkfield.22_.2845_nm.29 Core 2 Quad Q9550] | 2.83 | 4 | 1:06 | hippo_p3 | rev32 <!-- deathspud --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410] | 2.33 | 4 | 1:27 | hippo | rev32 |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410] | 2.33 | 4 | 1:31 | hippo_p3 | rev32 <!-- tinman --> |- | AMD | Phenom 9850 Quad-Core | 2.75 | 4 | 1:36 | hippo_p3 | rev32 <!-- greenwulf --> |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Opteron_microprocessors#Opteron_200-series_.22SledgeHammer.22_.28B3_.26_C0_.26_CG.2C_130_nm.29 Opteron 248] | 2.2 | 1 | 2:18 | hippo_p3 | rev32 <!-- gltph --> |- | Intel | Core Duo T2300 (Mac Mini) | 1.66 | 2 | 2:41 | hippo_p3 | rev32 <!-- abbondanza --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Prestonia.22_.28standard-voltage.2C_130_nm.29 Xeon 2.4] | 2.4 | 1 | 3:03 | hippo_p3 | rev26 <!-- timberwulf --> |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Athlon_XP_microprocessors#Athlon_XP_.22Palomino.22_.28Model_6.2C_180_nm.29 Athlon XP 1800+] | 1.53 | 1 | 4:30 | hippo_p3 | rev26 |} <small>(You don't ''have'' to link to the CPU wikipedia page; just put down whatever you got and even if you're unsure. If in doubt just put the output from cat /proc/cpuinfo | \ awk 'BEGIN {FS=":"}; \ /vendor_id/ {vendor=$2}; \ /model name/ {model=$2}; \ /cpu MHz/ {GHz=$2/1000}; \ /siblings/ {cores=$2}; \ END {printf("|-\n| %s\n| %s\n| %.1f\n| %d\n| TIME\n| ?\n| ?\n", vendor, model, GHz, cores)}' into the wiki table and replace ''TIME'' by what you measured.</small> 5b42c3288a5b999fbaf24233e97577bc49f0ec79 167 166 2008-11-21T01:35:28Z Oliver 2 Xeon Harpertown 2.5 GHz wikitext text/x-wiki As a basic performance test we run the simulations in the <tt>test</tt> directory with these commands (on Linux): cd testjobs time ./calc_testjobs <ul> <li>We report the ''user'' time.</li> <li>CPU properties are found with <pre>cat /proc/cpuinfo</pre> and model names from [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors List_of_Intel_microprocessors] for Intel (also see the [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors#Detailed_x86_architecture_microprocessor_lists detailed lists of Intel x86 cpus]) and [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors List_of_AMD_microprocessors] for AMD cpus (also see the [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors#Detailed_microprocessor_release_lists detailed lists of AMD cpus]).</li> <li>Also report the binary used (<tt>hippo</tt> or <tt>hippo_p3</tt>) and the revision.</li> <li>Note that these tests only utilize a ''single core''.</li> <li>These results only give a rough idea of the ''relative'' performance of different architectures.</li> </ul> Please add your own results. {| class="wikitable" |- ! vendor ! model ! GHz ! cores ! time/min ! binary ! revision |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Core_2_microprocessors#.22Yorkfield.22_.2845_nm.29 Core 2 Quad Q9550] | 2.83 | 4 | 1:04 | hippo | rev32 <!-- deathspud --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Core_2_microprocessors#.22Yorkfield.22_.2845_nm.29 Core 2 Quad Q9550] | 2.83 | 4 | 1:06 | hippo_p3 | rev32 <!-- deathspud --> |- | Intel | Quad Core Xeon E4520 | 2.5 | 4 | 1:25 | hippo | rev32 <!-- darthtater --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410] | 2.33 | 4 | 1:27 | hippo | rev32 |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410] | 2.33 | 4 | 1:31 | hippo_p3 | rev32 <!-- tinman --> |- | AMD | Phenom 9850 Quad-Core | 2.75 | 4 | 1:36 | hippo_p3 | rev32 <!-- greenwulf --> |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Opteron_microprocessors#Opteron_200-series_.22SledgeHammer.22_.28B3_.26_C0_.26_CG.2C_130_nm.29 Opteron 248] | 2.2 | 1 | 2:18 | hippo_p3 | rev32 <!-- gltph --> |- | Intel | Core Duo T2300 (Mac Mini) | 1.66 | 2 | 2:41 | hippo_p3 | rev32 <!-- abbondanza --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Prestonia.22_.28standard-voltage.2C_130_nm.29 Xeon 2.4] | 2.4 | 1 | 3:03 | hippo_p3 | rev26 <!-- timberwulf --> |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Athlon_XP_microprocessors#Athlon_XP_.22Palomino.22_.28Model_6.2C_180_nm.29 Athlon XP 1800+] | 1.53 | 1 | 4:30 | hippo_p3 | rev26 |} <small>(You don't ''have'' to link to the CPU wikipedia page; just put down whatever you got and even if you're unsure. If in doubt just put the output from cat /proc/cpuinfo | \ awk 'BEGIN {FS=":"}; \ /vendor_id/ {vendor=$2}; \ /model name/ {model=$2}; \ /cpu MHz/ {GHz=$2/1000}; \ /siblings/ {cores=$2}; \ END {printf("|-\n| %s\n| %s\n| %.1f\n| %d\n| TIME\n| ?\n| ?\n", vendor, model, GHz, cores)}' into the wiki table and replace ''TIME'' by what you measured.</small> 6fbe5345dd144ec040ff507d845c009f094733b0 168 167 2008-11-21T01:53:51Z Oliver 2 darthtater update (run on empty machine) wikitext text/x-wiki As a basic performance test we run the simulations in the <tt>test</tt> directory with these commands (on Linux): cd testjobs time ./calc_testjobs <ul> <li>We report the ''user'' time.</li> <li>CPU properties are found with <pre>cat /proc/cpuinfo</pre> and model names from [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors List_of_Intel_microprocessors] for Intel (also see the [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors#Detailed_x86_architecture_microprocessor_lists detailed lists of Intel x86 cpus]) and [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors List_of_AMD_microprocessors] for AMD cpus (also see the [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors#Detailed_microprocessor_release_lists detailed lists of AMD cpus]).</li> <li>Also report the binary used (<tt>hippo</tt> or <tt>hippo_p3</tt>) and the revision.</li> <li>Note that these tests only utilize a ''single core''.</li> <li>These results only give a rough idea of the ''relative'' performance of different architectures.</li> </ul> Please add your own results. {| class="wikitable" |- ! vendor ! model ! GHz ! cores ! time/min ! binary ! revision |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Core_2_microprocessors#.22Yorkfield.22_.2845_nm.29 Core 2 Quad Q9550] | 2.83 | 4 | 1:04 | hippo | rev32 <!-- deathspud --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Core_2_microprocessors#.22Yorkfield.22_.2845_nm.29 Core 2 Quad Q9550] | 2.83 | 4 | 1:06 | hippo_p3 | rev32 <!-- deathspud --> |- | Intel | Quad Core Xeon E4520 | 2.5 | 4 | 1:16 | hippo | rev32 <!-- darthtater --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410] | 2.33 | 4 | 1:27 | hippo | rev32 |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410] | 2.33 | 4 | 1:31 | hippo_p3 | rev32 <!-- tinman --> |- | AMD | Phenom 9850 Quad-Core | 2.75 | 4 | 1:36 | hippo_p3 | rev32 <!-- greenwulf --> |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Opteron_microprocessors#Opteron_200-series_.22SledgeHammer.22_.28B3_.26_C0_.26_CG.2C_130_nm.29 Opteron 248] | 2.2 | 1 | 2:18 | hippo_p3 | rev32 <!-- gltph --> |- | Intel | Core Duo T2300 (Mac Mini) | 1.66 | 2 | 2:41 | hippo_p3 | rev32 <!-- abbondanza --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Prestonia.22_.28standard-voltage.2C_130_nm.29 Xeon 2.4] | 2.4 | 1 | 3:03 | hippo_p3 | rev26 <!-- timberwulf --> |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Athlon_XP_microprocessors#Athlon_XP_.22Palomino.22_.28Model_6.2C_180_nm.29 Athlon XP 1800+] | 1.53 | 1 | 4:30 | hippo_p3 | rev26 |} <small>(You don't ''have'' to link to the CPU wikipedia page; just put down whatever you got and even if you're unsure. If in doubt just put the output from cat /proc/cpuinfo | \ awk 'BEGIN {FS=":"}; \ /vendor_id/ {vendor=$2}; \ /model name/ {model=$2}; \ /cpu MHz/ {GHz=$2/1000}; \ /siblings/ {cores=$2}; \ END {printf("|-\n| %s\n| %s\n| %.1f\n| %d\n| TIME\n| ?\n| ?\n", vendor, model, GHz, cores)}' into the wiki table and replace ''TIME'' by what you measured.</small> 51878608599172b37af806414316e72f1c0e326b 169 168 2008-11-21T02:08:52Z Oliver 2 wikitext text/x-wiki As a basic performance test we run the simulations in the <tt>test</tt> directory with these commands (on Linux): cd testjobs time ./calc_testjobs <ul> <li>We report the ''user'' time.</li> <li>CPU properties are found with <pre>cat /proc/cpuinfo</pre> and model names from [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors List_of_Intel_microprocessors] for Intel (also see the [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors#Detailed_x86_architecture_microprocessor_lists detailed lists of Intel x86 cpus]) and [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors List_of_AMD_microprocessors] for AMD cpus (also see the [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors#Detailed_microprocessor_release_lists detailed lists of AMD cpus]).</li> <li>Also report the binary used (<tt>hippo</tt> or <tt>hippo_p3</tt>) and the revision.</li> <li>Note that these tests only utilize a ''single core''.</li> <li>These results only give a rough idea of the ''relative'' performance of different architectures.</li> </ul> Please add your own results. {| class="wikitable" |- ! vendor ! model ! GHz ! cores ! time/min ! binary ! revision |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Core_2_microprocessors#.22Yorkfield.22_.2845_nm.29 Core 2 Quad Q9550] | 2.83 | 4 | 1:04 | hippo | rev32 <!-- deathspud --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Core_2_microprocessors#.22Yorkfield.22_.2845_nm.29 Core 2 Quad Q9550] | 2.83 | 4 | 1:06 | hippo_p3 | rev32 <!-- deathspud --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon E4520] | 2.5 | 4 | 1:16 | hippo | rev32 <!-- darthtater --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410] | 2.33 | 4 | 1:27 | hippo | rev32 |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410] | 2.33 | 4 | 1:31 | hippo_p3 | rev32 <!-- tinman --> |- | AMD | Phenom 9850 Quad-Core | 2.75 | 4 | 1:36 | hippo_p3 | rev32 <!-- greenwulf --> |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Opteron_microprocessors#Opteron_200-series_.22SledgeHammer.22_.28B3_.26_C0_.26_CG.2C_130_nm.29 Opteron 248] | 2.2 | 1 | 2:18 | hippo_p3 | rev32 <!-- gltph --> |- | Intel | Core Duo T2300 (Mac Mini) | 1.66 | 2 | 2:41 | hippo_p3 | rev32 <!-- abbondanza --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Prestonia.22_.28standard-voltage.2C_130_nm.29 Xeon 2.4] | 2.4 | 1 | 3:03 | hippo_p3 | rev26 <!-- timberwulf --> |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Athlon_XP_microprocessors#Athlon_XP_.22Palomino.22_.28Model_6.2C_180_nm.29 Athlon XP 1800+] | 1.53 | 1 | 4:30 | hippo_p3 | rev26 |} <small>(You don't ''have'' to link to the CPU wikipedia page; just put down whatever you got and even if you're unsure. If in doubt just put the output from cat /proc/cpuinfo | \ awk 'BEGIN {FS=":"}; \ /vendor_id/ {vendor=$2}; \ /model name/ {model=$2}; \ /cpu MHz/ {GHz=$2/1000}; \ /siblings/ {cores=$2}; \ END {printf("|-\n| %s\n| %s\n| %.1f\n| %d\n| TIME\n| ?\n| ?\n", vendor, model, GHz, cores)}' into the wiki table and replace ''TIME'' by what you measured.</small> f053f51083ae48f345b461187d2e35b8d73316aa 170 169 2008-11-21T02:10:37Z Oliver 2 wikitext text/x-wiki As a basic performance test we run the simulations in the <tt>test</tt> directory with these commands (on Linux): cd testjobs time ./calc_testjobs <ul> <li>We report the ''user'' time.</li> <li>CPU properties are found with <pre>cat /proc/cpuinfo</pre> and model names from [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors List_of_Intel_microprocessors] for Intel (also see the [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors#Detailed_x86_architecture_microprocessor_lists detailed lists of Intel x86 cpus]) and [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors List_of_AMD_microprocessors] for AMD cpus (also see the [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors#Detailed_microprocessor_release_lists detailed lists of AMD cpus]).</li> <li>Also report the binary used (<tt>hippo</tt> or <tt>hippo_p3</tt>) and the revision.</li> <li>Note that these tests only utilize a ''single core''.</li> <li>These results only give a rough idea of the ''relative'' performance of different architectures.</li> </ul> Please add your own results. {| class="wikitable" |- ! vendor ! model ! GHz ! cores ! time/min ! binary ! revision |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Core_2_microprocessors#.22Yorkfield.22_.2845_nm.29 Core 2 Quad Q9550] | 2.83 | 4 | 1:04 | hippo | rev32 <!-- deathspud --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Core_2_microprocessors#.22Yorkfield.22_.2845_nm.29 Core 2 Quad Q9550] | 2.83 | 4 | 1:06 | hippo_p3 | rev32 <!-- deathspud --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28standard-voltage.2C_45_nm.29 Quad Core Xeon E5420] | 2.5 | 4 | 1:16 | hippo | rev32 <!-- darthtater --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410] | 2.33 | 4 | 1:27 | hippo | rev32 |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410] | 2.33 | 4 | 1:31 | hippo_p3 | rev32 <!-- tinman --> |- | AMD | Phenom 9850 Quad-Core | 2.75 | 4 | 1:36 | hippo_p3 | rev32 <!-- greenwulf --> |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Opteron_microprocessors#Opteron_200-series_.22SledgeHammer.22_.28B3_.26_C0_.26_CG.2C_130_nm.29 Opteron 248] | 2.2 | 1 | 2:18 | hippo_p3 | rev32 <!-- gltph --> |- | Intel | Core Duo T2300 (Mac Mini) | 1.66 | 2 | 2:41 | hippo_p3 | rev32 <!-- abbondanza --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Prestonia.22_.28standard-voltage.2C_130_nm.29 Xeon 2.4] | 2.4 | 1 | 3:03 | hippo_p3 | rev26 <!-- timberwulf --> |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Athlon_XP_microprocessors#Athlon_XP_.22Palomino.22_.28Model_6.2C_180_nm.29 Athlon XP 1800+] | 1.53 | 1 | 4:30 | hippo_p3 | rev26 |} <small>(You don't ''have'' to link to the CPU wikipedia page; just put down whatever you got and even if you're unsure. If in doubt just put the output from cat /proc/cpuinfo | \ awk 'BEGIN {FS=":"}; \ /vendor_id/ {vendor=$2}; \ /model name/ {model=$2}; \ /cpu MHz/ {GHz=$2/1000}; \ /siblings/ {cores=$2}; \ END {printf("|-\n| %s\n| %s\n| %.1f\n| %d\n| TIME\n| ?\n| ?\n", vendor, model, GHz, cores)}' into the wiki table and replace ''TIME'' by what you measured.</small> f2be6ff40c6b78c7ba058a9a457319df96704024 171 170 2008-11-21T02:13:01Z Oliver 2 wikitext text/x-wiki As a basic performance test we run the simulations in the <tt>test</tt> directory with these commands (on Linux): cd testjobs time ./calc_testjobs <ul> <li>We report the ''user'' time.</li> <li>CPU properties are found with <pre>cat /proc/cpuinfo</pre> and model names from [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors List_of_Intel_microprocessors] for Intel (also see the [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors#Detailed_x86_architecture_microprocessor_lists detailed lists of Intel x86 cpus]) and [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors List_of_AMD_microprocessors] for AMD cpus (also see the [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors#Detailed_microprocessor_release_lists detailed lists of AMD cpus]).</li> <li>Also report the binary used (<tt>hippo</tt> or <tt>hippo_p3</tt>) and the revision.</li> <li>Note that these tests only utilize a ''single core''.</li> <li>These results only give a rough idea of the ''relative'' performance of different architectures.</li> </ul> Please add your own results. {| class="wikitable" |- ! vendor ! model ! GHz ! cores ! time/min ! binary ! revision |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Core_2_microprocessors#.22Yorkfield.22_.2845_nm.29 Core 2 Quad Q9550] | 2.83 | 4 | 1:04 | hippo | rev32 <!-- deathspud --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Core_2_microprocessors#.22Yorkfield.22_.2845_nm.29 Core 2 Quad Q9550] | 2.83 | 4 | 1:06 | hippo_p3 | rev32 <!-- deathspud --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28standard-voltage.2C_45_nm.29 Quad Core Xeon E5420] | 2.5 | 4 | 1:16 | hippo | rev32 <!-- darthtater --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410] | 2.33 | 4 | 1:27 | hippo | rev32 |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410] | 2.33 | 4 | 1:31 | hippo_p3 | rev32 <!-- tinman --> |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Phenom_microprocessors#.22Agena.22_.28B2_.26_B3.2C_65_nm.29 Phenom X4 9850] | 2.75 | 4 | 1:36 | hippo_p3 | rev32 <!-- greenwulf --> |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Opteron_microprocessors#Opteron_200-series_.22SledgeHammer.22_.28B3_.26_C0_.26_CG.2C_130_nm.29 Opteron 248] | 2.2 | 1 | 2:18 | hippo_p3 | rev32 <!-- gltph --> |- | Intel | Core Duo T2300 (Mac Mini) | 1.66 | 2 | 2:41 | hippo_p3 | rev32 <!-- abbondanza --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Prestonia.22_.28standard-voltage.2C_130_nm.29 Xeon 2.4] | 2.4 | 1 | 3:03 | hippo_p3 | rev26 <!-- timberwulf --> |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Athlon_XP_microprocessors#Athlon_XP_.22Palomino.22_.28Model_6.2C_180_nm.29 Athlon XP 1800+] | 1.53 | 1 | 4:30 | hippo_p3 | rev26 |} <small>(You don't ''have'' to link to the CPU wikipedia page; just put down whatever you got and even if you're unsure. If in doubt just put the output from cat /proc/cpuinfo | \ awk 'BEGIN {FS=":"}; \ /vendor_id/ {vendor=$2}; \ /model name/ {model=$2}; \ /cpu MHz/ {GHz=$2/1000}; \ /siblings/ {cores=$2}; \ END {printf("|-\n| %s\n| %s\n| %.1f\n| %d\n| TIME\n| ?\n| ?\n", vendor, model, GHz, cores)}' into the wiki table and replace ''TIME'' by what you measured.</small> 9530298f235c7bac821c8e68db7c67f0e7b0cd83 172 171 2008-11-21T14:51:04Z Kaihsu 10 try sortable wikitext text/x-wiki As a basic performance test we run the simulations in the <tt>test</tt> directory with these commands (on Linux): cd testjobs time ./calc_testjobs <ul> <li>We report the ''user'' time.</li> <li>CPU properties are found with <pre>cat /proc/cpuinfo</pre> and model names from [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors List_of_Intel_microprocessors] for Intel (also see the [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors#Detailed_x86_architecture_microprocessor_lists detailed lists of Intel x86 cpus]) and [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors List_of_AMD_microprocessors] for AMD cpus (also see the [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors#Detailed_microprocessor_release_lists detailed lists of AMD cpus]).</li> <li>Also report the binary used (<tt>hippo</tt> or <tt>hippo_p3</tt>) and the revision.</li> <li>Note that these tests only utilize a ''single core''.</li> <li>These results only give a rough idea of the ''relative'' performance of different architectures.</li> </ul> Please add your own results. {| class="wikitable sortable" |- ! vendor ! model ! GHz ! cores ! time/min ! binary ! revision |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Core_2_microprocessors#.22Yorkfield.22_.2845_nm.29 Core 2 Quad Q9550] | 2.83 | 4 | 1:04 | hippo | rev32 <!-- deathspud --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Core_2_microprocessors#.22Yorkfield.22_.2845_nm.29 Core 2 Quad Q9550] | 2.83 | 4 | 1:06 | hippo_p3 | rev32 <!-- deathspud --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28standard-voltage.2C_45_nm.29 Quad Core Xeon E5420] | 2.5 | 4 | 1:16 | hippo | rev32 <!-- darthtater --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410] | 2.33 | 4 | 1:27 | hippo | rev32 |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410] | 2.33 | 4 | 1:31 | hippo_p3 | rev32 <!-- tinman --> |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Phenom_microprocessors#.22Agena.22_.28B2_.26_B3.2C_65_nm.29 Phenom X4 9850] | 2.75 | 4 | 1:36 | hippo_p3 | rev32 <!-- greenwulf --> |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Opteron_microprocessors#Opteron_200-series_.22SledgeHammer.22_.28B3_.26_C0_.26_CG.2C_130_nm.29 Opteron 248] | 2.2 | 1 | 2:18 | hippo_p3 | rev32 <!-- gltph --> |- | Intel | Core Duo T2300 (Mac Mini) | 1.66 | 2 | 2:41 | hippo_p3 | rev32 <!-- abbondanza --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Prestonia.22_.28standard-voltage.2C_130_nm.29 Xeon 2.4] | 2.4 | 1 | 3:03 | hippo_p3 | rev26 <!-- timberwulf --> |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Athlon_XP_microprocessors#Athlon_XP_.22Palomino.22_.28Model_6.2C_180_nm.29 Athlon XP 1800+] | 1.53 | 1 | 4:30 | hippo_p3 | rev26 |} <small>(You don't ''have'' to link to the CPU wikipedia page; just put down whatever you got and even if you're unsure. If in doubt just put the output from cat /proc/cpuinfo | \ awk 'BEGIN {FS=":"}; \ /vendor_id/ {vendor=$2}; \ /model name/ {model=$2}; \ /cpu MHz/ {GHz=$2/1000}; \ /siblings/ {cores=$2}; \ END {printf("|-\n| %s\n| %s\n| %.1f\n| %d\n| TIME\n| ?\n| ?\n", vendor, model, GHz, cores)}' into the wiki table and replace ''TIME'' by what you measured.</small> 38cb0b83107224597230ac9175d6db4b5b9c63f6 173 172 2008-11-21T14:54:26Z Kaihsu 10 wikitext text/x-wiki As a basic performance test we run the simulations in the <tt>test</tt> directory with these commands (on Linux): cd testjobs time ./calc_testjobs <ul> <li>We report the ''user'' time.</li> <li>CPU properties are found with <pre>cat /proc/cpuinfo</pre> and model names from [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors List of Intelmicroprocessors] for Intel (also see the [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors#Detailed_x86_architecture_microprocessor_lists detailed lists of Intel x86 cpus]) and [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors List of AMD microprocessors] for AMD cpus (also see the [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors#Detailed_microprocessor_release_lists detailed lists of AMD CPUs]).</li> <li>Also report the binary used (<tt>hippo</tt> or <tt>hippo_p3</tt>) and the revision.</li> <li>Note that these tests only utilize a ''single core''.</li> <li>These results only give a rough idea of the ''relative'' performance of different architectures.</li> </ul> Please add your own results. {| class="wikitable sortable" |- ! vendor ! model ! GHz ! cores ! time/min ! binary ! revision |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Core_2_microprocessors#.22Yorkfield.22_.2845_nm.29 Core 2 Quad Q9550] | 2.83 | 4 | 1:04 | hippo | rev32 <!-- deathspud --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Core_2_microprocessors#.22Yorkfield.22_.2845_nm.29 Core 2 Quad Q9550] | 2.83 | 4 | 1:06 | hippo_p3 | rev32 <!-- deathspud --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28standard-voltage.2C_45_nm.29 Quad Core Xeon E5420] | 2.5 | 4 | 1:16 | hippo | rev32 <!-- darthtater --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410] | 2.33 | 4 | 1:27 | hippo | rev32 |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410] | 2.33 | 4 | 1:31 | hippo_p3 | rev32 <!-- tinman --> |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Phenom_microprocessors#.22Agena.22_.28B2_.26_B3.2C_65_nm.29 Phenom X4 9850] | 2.75 | 4 | 1:36 | hippo_p3 | rev32 <!-- greenwulf --> |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Opteron_microprocessors#Opteron_200-series_.22SledgeHammer.22_.28B3_.26_C0_.26_CG.2C_130_nm.29 Opteron 248] | 2.2 | 1 | 2:18 | hippo_p3 | rev32 <!-- gltph --> |- | Intel | Core Duo T2300 (Mac Mini) | 1.66 | 2 | 2:41 | hippo_p3 | rev32 <!-- abbondanza --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Prestonia.22_.28standard-voltage.2C_130_nm.29 Xeon 2.4] | 2.4 | 1 | 3:03 | hippo_p3 | rev26 <!-- timberwulf --> |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Athlon_XP_microprocessors#Athlon_XP_.22Palomino.22_.28Model_6.2C_180_nm.29 Athlon XP 1800+] | 1.53 | 1 | 4:30 | hippo_p3 | rev26 |} <small>(You don't ''have'' to link to the CPU wikipedia page; just put down whatever you got and even if you're unsure. If in doubt just put the output from cat /proc/cpuinfo | \ awk 'BEGIN {FS=":"}; \ /vendor_id/ {vendor=$2}; \ /model name/ {model=$2}; \ /cpu MHz/ {GHz=$2/1000}; \ /siblings/ {cores=$2}; \ END {printf("|-\n| %s\n| %s\n| %.1f\n| %d\n| TIME\n| ?\n| ?\n", vendor, model, GHz, cores)}' into the wiki table and replace ''TIME'' by what you measured.</small> 3191a4399776278ca66e7da4db33d22f7e8a6786 174 173 2008-11-21T14:54:49Z Kaihsu 10 wikitext text/x-wiki As a basic performance test we run the simulations in the <tt>test</tt> directory with these commands (on Linux): cd testjobs time ./calc_testjobs <ul> <li>We report the ''user'' time.</li> <li>CPU properties are found with <pre>cat /proc/cpuinfo</pre> and model names from [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors List of Intelmicroprocessors] for Intel (also see the [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors#Detailed_x86_architecture_microprocessor_lists detailed lists of Intel x86 CPUs]) and [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors List of AMD microprocessors] for AMD cpus (also see the [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors#Detailed_microprocessor_release_lists detailed lists of AMD CPUs]).</li> <li>Also report the binary used (<tt>hippo</tt> or <tt>hippo_p3</tt>) and the revision.</li> <li>Note that these tests only utilize a ''single core''.</li> <li>These results only give a rough idea of the ''relative'' performance of different architectures.</li> </ul> Please add your own results. {| class="wikitable sortable" |- ! vendor ! model ! GHz ! cores ! time/min ! binary ! revision |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Core_2_microprocessors#.22Yorkfield.22_.2845_nm.29 Core 2 Quad Q9550] | 2.83 | 4 | 1:04 | hippo | rev32 <!-- deathspud --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Core_2_microprocessors#.22Yorkfield.22_.2845_nm.29 Core 2 Quad Q9550] | 2.83 | 4 | 1:06 | hippo_p3 | rev32 <!-- deathspud --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28standard-voltage.2C_45_nm.29 Quad Core Xeon E5420] | 2.5 | 4 | 1:16 | hippo | rev32 <!-- darthtater --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410] | 2.33 | 4 | 1:27 | hippo | rev32 |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410] | 2.33 | 4 | 1:31 | hippo_p3 | rev32 <!-- tinman --> |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Phenom_microprocessors#.22Agena.22_.28B2_.26_B3.2C_65_nm.29 Phenom X4 9850] | 2.75 | 4 | 1:36 | hippo_p3 | rev32 <!-- greenwulf --> |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Opteron_microprocessors#Opteron_200-series_.22SledgeHammer.22_.28B3_.26_C0_.26_CG.2C_130_nm.29 Opteron 248] | 2.2 | 1 | 2:18 | hippo_p3 | rev32 <!-- gltph --> |- | Intel | Core Duo T2300 (Mac Mini) | 1.66 | 2 | 2:41 | hippo_p3 | rev32 <!-- abbondanza --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Prestonia.22_.28standard-voltage.2C_130_nm.29 Xeon 2.4] | 2.4 | 1 | 3:03 | hippo_p3 | rev26 <!-- timberwulf --> |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Athlon_XP_microprocessors#Athlon_XP_.22Palomino.22_.28Model_6.2C_180_nm.29 Athlon XP 1800+] | 1.53 | 1 | 4:30 | hippo_p3 | rev26 |} <small>(You don't ''have'' to link to the CPU wikipedia page; just put down whatever you got and even if you're unsure. If in doubt just put the output from cat /proc/cpuinfo | \ awk 'BEGIN {FS=":"}; \ /vendor_id/ {vendor=$2}; \ /model name/ {model=$2}; \ /cpu MHz/ {GHz=$2/1000}; \ /siblings/ {cores=$2}; \ END {printf("|-\n| %s\n| %s\n| %.1f\n| %d\n| TIME\n| ?\n| ?\n", vendor, model, GHz, cores)}' into the wiki table and replace ''TIME'' by what you measured.</small> 0261edfaad600f3e4c72d3140c96398e93af8bd4 175 174 2008-12-07T12:20:18Z Oliver 2 rev35 wikitext text/x-wiki As a basic performance test we run the simulations in the <tt>test</tt> directory with these commands (on Linux): cd testjobs time ./calc_testjobs <ul> <li>We report the ''user'' time.</li> <li>CPU properties are found with <pre>cat /proc/cpuinfo</pre> and model names from [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors List of Intelmicroprocessors] for Intel (also see the [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors#Detailed_x86_architecture_microprocessor_lists detailed lists of Intel x86 CPUs]) and [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors List of AMD microprocessors] for AMD cpus (also see the [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors#Detailed_microprocessor_release_lists detailed lists of AMD CPUs]).</li> <li>Also report the binary used (<tt>hippo</tt> or <tt>hippo_p3</tt>) and the revision.</li> <li>Note that these tests only utilize a ''single core''.</li> <li>These results only give a rough idea of the ''relative'' performance of different architectures.</li> </ul> Please add your own results. {| class="wikitable sortable" |- ! vendor ! model ! GHz ! cores ! time/min ! binary ! revision |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Core_2_microprocessors#.22Yorkfield.22_.2845_nm.29 Core 2 Quad Q9550] | 2.83 | 4 | 1:04 | hippo | rev32 <!-- deathspud --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Core_2_microprocessors#.22Yorkfield.22_.2845_nm.29 Core 2 Quad Q9550] | 2.83 | 4 | 1:06 | hippo_p3 | rev32 <!-- deathspud --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28standard-voltage.2C_45_nm.29 Quad Core Xeon E5420] | 2.5 | 4 | 1:16 | hippo | rev35 <!-- darthtater --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28standard-voltage.2C_45_nm.29 Quad Core Xeon E5420] | 2.5 | 4 | 1:16 | hippo | rev32 <!-- darthtater --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410] | 2.33 | 4 | 1:27 | hippo | rev32 |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410] | 2.33 | 4 | 1:31 | hippo_p3 | rev32 <!-- tinman --> |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Phenom_microprocessors#.22Agena.22_.28B2_.26_B3.2C_65_nm.29 Phenom X4 9850] | 2.75 | 4 | 1:36 | hippo_p3 | rev32 <!-- greenwulf --> |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Opteron_microprocessors#Opteron_200-series_.22SledgeHammer.22_.28B3_.26_C0_.26_CG.2C_130_nm.29 Opteron 248] | 2.2 | 1 | 2:18 | hippo_p3 | rev32 <!-- gltph --> |- | Intel | Core Duo T2300 (Mac Mini) | 1.66 | 2 | 2:41 | hippo_p3 | rev32 <!-- abbondanza --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Prestonia.22_.28standard-voltage.2C_130_nm.29 Xeon 2.4] | 2.4 | 1 | 3:03 | hippo_p3 | rev26 <!-- timberwulf --> |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Athlon_XP_microprocessors#Athlon_XP_.22Palomino.22_.28Model_6.2C_180_nm.29 Athlon XP 1800+] | 1.53 | 1 | 4:30 | hippo_p3 | rev26 |} <small>(You don't ''have'' to link to the CPU wikipedia page; just put down whatever you got and even if you're unsure. If in doubt just put the output from cat /proc/cpuinfo | \ awk 'BEGIN {FS=":"}; \ /vendor_id/ {vendor=$2}; \ /model name/ {model=$2}; \ /cpu MHz/ {GHz=$2/1000}; \ /siblings/ {cores=$2}; \ END {printf("|-\n| %s\n| %s\n| %.1f\n| %d\n| TIME\n| ?\n| ?\n", vendor, model, GHz, cores)}' into the wiki table and replace ''TIME'' by what you measured.</small> b23c7950d842eeb36117a0407db502d1425f106d 183 175 2008-12-07T15:33:21Z Oliver 2 /* Scaling */ wikitext text/x-wiki == Single processor performance == As a basic performance test we run the simulations in the <tt>test</tt> directory with these commands (on Linux): cd testjobs time ./calc_testjobs <ul> <li>We report the ''user'' time.</li> <li>CPU properties are found with <pre>cat /proc/cpuinfo</pre> and model names from [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors List of Intelmicroprocessors] for Intel (also see the [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors#Detailed_x86_architecture_microprocessor_lists detailed lists of Intel x86 CPUs]) and [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors List of AMD microprocessors] for AMD cpus (also see the [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors#Detailed_microprocessor_release_lists detailed lists of AMD CPUs]).</li> <li>Also report the binary used (<tt>hippo</tt> or <tt>hippo_p3</tt>) and the revision.</li> <li>Note that these tests only utilize a ''single core''.</li> <li>These results only give a rough idea of the ''relative'' performance of different architectures.</li> </ul> Please add your own results. {| class="wikitable sortable" |- ! vendor ! model ! GHz ! cores ! time/min ! binary ! revision |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Core_2_microprocessors#.22Yorkfield.22_.2845_nm.29 Core 2 Quad Q9550] | 2.83 | 4 | 1:04 | hippo | rev32 <!-- deathspud --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Core_2_microprocessors#.22Yorkfield.22_.2845_nm.29 Core 2 Quad Q9550] | 2.83 | 4 | 1:06 | hippo_p3 | rev32 <!-- deathspud --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28standard-voltage.2C_45_nm.29 Quad Core Xeon E5420] | 2.5 | 4 | 1:16 | hippo | rev35 <!-- darthtater --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28standard-voltage.2C_45_nm.29 Quad Core Xeon E5420] | 2.5 | 4 | 1:16 | hippo | rev32 <!-- darthtater --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410] | 2.33 | 4 | 1:27 | hippo | rev32 |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410] | 2.33 | 4 | 1:31 | hippo_p3 | rev32 <!-- tinman --> |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Phenom_microprocessors#.22Agena.22_.28B2_.26_B3.2C_65_nm.29 Phenom X4 9850] | 2.75 | 4 | 1:36 | hippo_p3 | rev32 <!-- greenwulf --> |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Opteron_microprocessors#Opteron_200-series_.22SledgeHammer.22_.28B3_.26_C0_.26_CG.2C_130_nm.29 Opteron 248] | 2.2 | 1 | 2:18 | hippo_p3 | rev32 <!-- gltph --> |- | Intel | Core Duo T2300 (Mac Mini) | 1.66 | 2 | 2:41 | hippo_p3 | rev32 <!-- abbondanza --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Prestonia.22_.28standard-voltage.2C_130_nm.29 Xeon 2.4] | 2.4 | 1 | 3:03 | hippo_p3 | rev26 <!-- timberwulf --> |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Athlon_XP_microprocessors#Athlon_XP_.22Palomino.22_.28Model_6.2C_180_nm.29 Athlon XP 1800+] | 1.53 | 1 | 4:30 | hippo_p3 | rev26 |} <small>(You don't ''have'' to link to the CPU wikipedia page; just put down whatever you got and even if you're unsure. If in doubt just put the output from cat /proc/cpuinfo | \ awk 'BEGIN {FS=":"}; \ /vendor_id/ {vendor=$2}; \ /model name/ {model=$2}; \ /cpu MHz/ {GHz=$2/1000}; \ /siblings/ {cores=$2}; \ END {printf("|-\n| %s\n| %s\n| %.1f\n| %d\n| TIME\n| ?\n| ?\n", vendor, model, GHz, cores)}' into the wiki table and replace ''TIME'' by what you measured.</small> == Scaling == All tests were run with Hippo beta rev35 on empty systems. See remarks on the [[Talk:Performance#Scaling|test methodology]]. [[Image:Scaling Q9550.png|Intel Quad Core Q9550]] 5b41ad35036b67493fcdbbad6a86dd6d750545e2 184 183 2008-12-07T15:34:33Z Oliver 2 /* Scaling */ wikitext text/x-wiki == Single processor performance == As a basic performance test we run the simulations in the <tt>test</tt> directory with these commands (on Linux): cd testjobs time ./calc_testjobs <ul> <li>We report the ''user'' time.</li> <li>CPU properties are found with <pre>cat /proc/cpuinfo</pre> and model names from [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors List of Intelmicroprocessors] for Intel (also see the [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors#Detailed_x86_architecture_microprocessor_lists detailed lists of Intel x86 CPUs]) and [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors List of AMD microprocessors] for AMD cpus (also see the [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors#Detailed_microprocessor_release_lists detailed lists of AMD CPUs]).</li> <li>Also report the binary used (<tt>hippo</tt> or <tt>hippo_p3</tt>) and the revision.</li> <li>Note that these tests only utilize a ''single core''.</li> <li>These results only give a rough idea of the ''relative'' performance of different architectures.</li> </ul> Please add your own results. {| class="wikitable sortable" |- ! vendor ! model ! GHz ! cores ! time/min ! binary ! revision |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Core_2_microprocessors#.22Yorkfield.22_.2845_nm.29 Core 2 Quad Q9550] | 2.83 | 4 | 1:04 | hippo | rev32 <!-- deathspud --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Core_2_microprocessors#.22Yorkfield.22_.2845_nm.29 Core 2 Quad Q9550] | 2.83 | 4 | 1:06 | hippo_p3 | rev32 <!-- deathspud --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28standard-voltage.2C_45_nm.29 Quad Core Xeon E5420] | 2.5 | 4 | 1:16 | hippo | rev35 <!-- darthtater --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28standard-voltage.2C_45_nm.29 Quad Core Xeon E5420] | 2.5 | 4 | 1:16 | hippo | rev32 <!-- darthtater --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410] | 2.33 | 4 | 1:27 | hippo | rev32 |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410] | 2.33 | 4 | 1:31 | hippo_p3 | rev32 <!-- tinman --> |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Phenom_microprocessors#.22Agena.22_.28B2_.26_B3.2C_65_nm.29 Phenom X4 9850] | 2.75 | 4 | 1:36 | hippo_p3 | rev32 <!-- greenwulf --> |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Opteron_microprocessors#Opteron_200-series_.22SledgeHammer.22_.28B3_.26_C0_.26_CG.2C_130_nm.29 Opteron 248] | 2.2 | 1 | 2:18 | hippo_p3 | rev32 <!-- gltph --> |- | Intel | Core Duo T2300 (Mac Mini) | 1.66 | 2 | 2:41 | hippo_p3 | rev32 <!-- abbondanza --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Prestonia.22_.28standard-voltage.2C_130_nm.29 Xeon 2.4] | 2.4 | 1 | 3:03 | hippo_p3 | rev26 <!-- timberwulf --> |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Athlon_XP_microprocessors#Athlon_XP_.22Palomino.22_.28Model_6.2C_180_nm.29 Athlon XP 1800+] | 1.53 | 1 | 4:30 | hippo_p3 | rev26 |} <small>(You don't ''have'' to link to the CPU wikipedia page; just put down whatever you got and even if you're unsure. If in doubt just put the output from cat /proc/cpuinfo | \ awk 'BEGIN {FS=":"}; \ /vendor_id/ {vendor=$2}; \ /model name/ {model=$2}; \ /cpu MHz/ {GHz=$2/1000}; \ /siblings/ {cores=$2}; \ END {printf("|-\n| %s\n| %s\n| %.1f\n| %d\n| TIME\n| ?\n| ?\n", vendor, model, GHz, cores)}' into the wiki table and replace ''TIME'' by what you measured.</small> == Scaling == All tests were run with Hippo beta rev35 on empty systems. See remarks on the [[Talk:Performance#Scaling|test methodology]]. [[Image:Scaling Q9550.png|frame|Intel Quad Core Q9550]] 440928168b4694bd8bf3c957e8e5a97ae37d22ca 186 184 2008-12-07T15:39:04Z Oliver 2 /* Scaling */ wikitext text/x-wiki == Single processor performance == As a basic performance test we run the simulations in the <tt>test</tt> directory with these commands (on Linux): cd testjobs time ./calc_testjobs <ul> <li>We report the ''user'' time.</li> <li>CPU properties are found with <pre>cat /proc/cpuinfo</pre> and model names from [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors List of Intelmicroprocessors] for Intel (also see the [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors#Detailed_x86_architecture_microprocessor_lists detailed lists of Intel x86 CPUs]) and [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors List of AMD microprocessors] for AMD cpus (also see the [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors#Detailed_microprocessor_release_lists detailed lists of AMD CPUs]).</li> <li>Also report the binary used (<tt>hippo</tt> or <tt>hippo_p3</tt>) and the revision.</li> <li>Note that these tests only utilize a ''single core''.</li> <li>These results only give a rough idea of the ''relative'' performance of different architectures.</li> </ul> Please add your own results. {| class="wikitable sortable" |- ! vendor ! model ! GHz ! cores ! time/min ! binary ! revision |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Core_2_microprocessors#.22Yorkfield.22_.2845_nm.29 Core 2 Quad Q9550] | 2.83 | 4 | 1:04 | hippo | rev32 <!-- deathspud --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Core_2_microprocessors#.22Yorkfield.22_.2845_nm.29 Core 2 Quad Q9550] | 2.83 | 4 | 1:06 | hippo_p3 | rev32 <!-- deathspud --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28standard-voltage.2C_45_nm.29 Quad Core Xeon E5420] | 2.5 | 4 | 1:16 | hippo | rev35 <!-- darthtater --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28standard-voltage.2C_45_nm.29 Quad Core Xeon E5420] | 2.5 | 4 | 1:16 | hippo | rev32 <!-- darthtater --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410] | 2.33 | 4 | 1:27 | hippo | rev32 |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410] | 2.33 | 4 | 1:31 | hippo_p3 | rev32 <!-- tinman --> |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Phenom_microprocessors#.22Agena.22_.28B2_.26_B3.2C_65_nm.29 Phenom X4 9850] | 2.75 | 4 | 1:36 | hippo_p3 | rev32 <!-- greenwulf --> |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Opteron_microprocessors#Opteron_200-series_.22SledgeHammer.22_.28B3_.26_C0_.26_CG.2C_130_nm.29 Opteron 248] | 2.2 | 1 | 2:18 | hippo_p3 | rev32 <!-- gltph --> |- | Intel | Core Duo T2300 (Mac Mini) | 1.66 | 2 | 2:41 | hippo_p3 | rev32 <!-- abbondanza --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Prestonia.22_.28standard-voltage.2C_130_nm.29 Xeon 2.4] | 2.4 | 1 | 3:03 | hippo_p3 | rev26 <!-- timberwulf --> |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Athlon_XP_microprocessors#Athlon_XP_.22Palomino.22_.28Model_6.2C_180_nm.29 Athlon XP 1800+] | 1.53 | 1 | 4:30 | hippo_p3 | rev26 |} <small>(You don't ''have'' to link to the CPU wikipedia page; just put down whatever you got and even if you're unsure. If in doubt just put the output from cat /proc/cpuinfo | \ awk 'BEGIN {FS=":"}; \ /vendor_id/ {vendor=$2}; \ /model name/ {model=$2}; \ /cpu MHz/ {GHz=$2/1000}; \ /siblings/ {cores=$2}; \ END {printf("|-\n| %s\n| %s\n| %.1f\n| %d\n| TIME\n| ?\n| ?\n", vendor, model, GHz, cores)}' into the wiki table and replace ''TIME'' by what you measured.</small> == Scaling == All tests were run with Hippo beta rev35 on empty systems. See remarks on the [[Talk:Performance#Scaling|test methodology]]. [[Image:Scaling Q9550.png|thumb|400px|left|Intel Quad Core Q9550 2.8 GHz]] [[Image:Scaling E5420.png|thumb|400px|right|Dual Intel Quad Core Xeon E5420 2.5 GHz]] f7a71c1e0082c8bf6875c4010c32a67e2cb03b32 197 186 2008-12-07T21:15:08Z Oliver 2 /* Scaling */ Phenom wikitext text/x-wiki == Single processor performance == As a basic performance test we run the simulations in the <tt>test</tt> directory with these commands (on Linux): cd testjobs time ./calc_testjobs <ul> <li>We report the ''user'' time.</li> <li>CPU properties are found with <pre>cat /proc/cpuinfo</pre> and model names from [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors List of Intelmicroprocessors] for Intel (also see the [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors#Detailed_x86_architecture_microprocessor_lists detailed lists of Intel x86 CPUs]) and [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors List of AMD microprocessors] for AMD cpus (also see the [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors#Detailed_microprocessor_release_lists detailed lists of AMD CPUs]).</li> <li>Also report the binary used (<tt>hippo</tt> or <tt>hippo_p3</tt>) and the revision.</li> <li>Note that these tests only utilize a ''single core''.</li> <li>These results only give a rough idea of the ''relative'' performance of different architectures.</li> </ul> Please add your own results. {| class="wikitable sortable" |- ! vendor ! model ! GHz ! cores ! time/min ! binary ! revision |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Core_2_microprocessors#.22Yorkfield.22_.2845_nm.29 Core 2 Quad Q9550] | 2.83 | 4 | 1:04 | hippo | rev32 <!-- deathspud --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Core_2_microprocessors#.22Yorkfield.22_.2845_nm.29 Core 2 Quad Q9550] | 2.83 | 4 | 1:06 | hippo_p3 | rev32 <!-- deathspud --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28standard-voltage.2C_45_nm.29 Quad Core Xeon E5420] | 2.5 | 4 | 1:16 | hippo | rev35 <!-- darthtater --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28standard-voltage.2C_45_nm.29 Quad Core Xeon E5420] | 2.5 | 4 | 1:16 | hippo | rev32 <!-- darthtater --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410] | 2.33 | 4 | 1:27 | hippo | rev32 |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410] | 2.33 | 4 | 1:31 | hippo_p3 | rev32 <!-- tinman --> |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Phenom_microprocessors#.22Agena.22_.28B2_.26_B3.2C_65_nm.29 Phenom X4 9850] | 2.75 | 4 | 1:36 | hippo_p3 | rev32 <!-- greenwulf --> |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Opteron_microprocessors#Opteron_200-series_.22SledgeHammer.22_.28B3_.26_C0_.26_CG.2C_130_nm.29 Opteron 248] | 2.2 | 1 | 2:18 | hippo_p3 | rev32 <!-- gltph --> |- | Intel | Core Duo T2300 (Mac Mini) | 1.66 | 2 | 2:41 | hippo_p3 | rev32 <!-- abbondanza --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Prestonia.22_.28standard-voltage.2C_130_nm.29 Xeon 2.4] | 2.4 | 1 | 3:03 | hippo_p3 | rev26 <!-- timberwulf --> |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Athlon_XP_microprocessors#Athlon_XP_.22Palomino.22_.28Model_6.2C_180_nm.29 Athlon XP 1800+] | 1.53 | 1 | 4:30 | hippo_p3 | rev26 |} <small>(You don't ''have'' to link to the CPU wikipedia page; just put down whatever you got and even if you're unsure. If in doubt just put the output from cat /proc/cpuinfo | \ awk 'BEGIN {FS=":"}; \ /vendor_id/ {vendor=$2}; \ /model name/ {model=$2}; \ /cpu MHz/ {GHz=$2/1000}; \ /siblings/ {cores=$2}; \ END {printf("|-\n| %s\n| %s\n| %.1f\n| %d\n| TIME\n| ?\n| ?\n", vendor, model, GHz, cores)}' into the wiki table and replace ''TIME'' by what you measured.</small> == Scaling == All tests were run with Hippo beta rev35 on empty systems. See remarks on the [[Talk:Performance#Scaling|test methodology]]. [[Image:Scaling Q9550.png|thumb|400px|left|Intel Quad Core Q9550 2.8 GHz]] [[Image:Scaling E5420.png|thumb|400px|right|Dual Intel Quad Core Xeon E5420 2.5 GHz]] [[Image:Scaling AMD X4 9840.png|thumb|400px|left|AMD Phenom X4 9850 Quad Core 2.5 GHz]] 554163a67947714510b0339dbc8a99e842119865 198 197 2008-12-07T21:15:37Z Oliver 2 fixed Phenom GHz wikitext text/x-wiki == Single processor performance == As a basic performance test we run the simulations in the <tt>test</tt> directory with these commands (on Linux): cd testjobs time ./calc_testjobs <ul> <li>We report the ''user'' time.</li> <li>CPU properties are found with <pre>cat /proc/cpuinfo</pre> and model names from [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors List of Intelmicroprocessors] for Intel (also see the [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors#Detailed_x86_architecture_microprocessor_lists detailed lists of Intel x86 CPUs]) and [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors List of AMD microprocessors] for AMD cpus (also see the [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors#Detailed_microprocessor_release_lists detailed lists of AMD CPUs]).</li> <li>Also report the binary used (<tt>hippo</tt> or <tt>hippo_p3</tt>) and the revision.</li> <li>Note that these tests only utilize a ''single core''.</li> <li>These results only give a rough idea of the ''relative'' performance of different architectures.</li> </ul> Please add your own results. {| class="wikitable sortable" |- ! vendor ! model ! GHz ! cores ! time/min ! binary ! revision |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Core_2_microprocessors#.22Yorkfield.22_.2845_nm.29 Core 2 Quad Q9550] | 2.83 | 4 | 1:04 | hippo | rev32 <!-- deathspud --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Core_2_microprocessors#.22Yorkfield.22_.2845_nm.29 Core 2 Quad Q9550] | 2.83 | 4 | 1:06 | hippo_p3 | rev32 <!-- deathspud --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28standard-voltage.2C_45_nm.29 Quad Core Xeon E5420] | 2.5 | 4 | 1:16 | hippo | rev35 <!-- darthtater --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28standard-voltage.2C_45_nm.29 Quad Core Xeon E5420] | 2.5 | 4 | 1:16 | hippo | rev32 <!-- darthtater --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410] | 2.33 | 4 | 1:27 | hippo | rev32 |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410] | 2.33 | 4 | 1:31 | hippo_p3 | rev32 <!-- tinman --> |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Phenom_microprocessors#.22Agena.22_.28B2_.26_B3.2C_65_nm.29 Phenom X4 9850] | 2.5 | 4 | 1:36 | hippo_p3 | rev32 <!-- greenwulf --> |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Opteron_microprocessors#Opteron_200-series_.22SledgeHammer.22_.28B3_.26_C0_.26_CG.2C_130_nm.29 Opteron 248] | 2.2 | 1 | 2:18 | hippo_p3 | rev32 <!-- gltph --> |- | Intel | Core Duo T2300 (Mac Mini) | 1.66 | 2 | 2:41 | hippo_p3 | rev32 <!-- abbondanza --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Prestonia.22_.28standard-voltage.2C_130_nm.29 Xeon 2.4] | 2.4 | 1 | 3:03 | hippo_p3 | rev26 <!-- timberwulf --> |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Athlon_XP_microprocessors#Athlon_XP_.22Palomino.22_.28Model_6.2C_180_nm.29 Athlon XP 1800+] | 1.53 | 1 | 4:30 | hippo_p3 | rev26 |} <small>(You don't ''have'' to link to the CPU wikipedia page; just put down whatever you got and even if you're unsure. If in doubt just put the output from cat /proc/cpuinfo | \ awk 'BEGIN {FS=":"}; \ /vendor_id/ {vendor=$2}; \ /model name/ {model=$2}; \ /cpu MHz/ {GHz=$2/1000}; \ /siblings/ {cores=$2}; \ END {printf("|-\n| %s\n| %s\n| %.1f\n| %d\n| TIME\n| ?\n| ?\n", vendor, model, GHz, cores)}' into the wiki table and replace ''TIME'' by what you measured.</small> == Scaling == All tests were run with Hippo beta rev35 on empty systems. See remarks on the [[Talk:Performance#Scaling|test methodology]]. [[Image:Scaling Q9550.png|thumb|400px|left|Intel Quad Core Q9550 2.8 GHz]] [[Image:Scaling E5420.png|thumb|400px|right|Dual Intel Quad Core Xeon E5420 2.5 GHz]] [[Image:Scaling AMD X4 9840.png|thumb|400px|left|AMD Phenom X4 9850 Quad Core 2.5 GHz]] 6fd6da3af8695165a3c5b60f7feb9f0117d1524f 199 198 2008-12-08T10:21:08Z Oliver 2 /* Scaling */ wikitext text/x-wiki == Single processor performance == As a basic performance test we run the simulations in the <tt>test</tt> directory with these commands (on Linux): cd testjobs time ./calc_testjobs <ul> <li>We report the ''user'' time.</li> <li>CPU properties are found with <pre>cat /proc/cpuinfo</pre> and model names from [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors List of Intelmicroprocessors] for Intel (also see the [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors#Detailed_x86_architecture_microprocessor_lists detailed lists of Intel x86 CPUs]) and [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors List of AMD microprocessors] for AMD cpus (also see the [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors#Detailed_microprocessor_release_lists detailed lists of AMD CPUs]).</li> <li>Also report the binary used (<tt>hippo</tt> or <tt>hippo_p3</tt>) and the revision.</li> <li>Note that these tests only utilize a ''single core''.</li> <li>These results only give a rough idea of the ''relative'' performance of different architectures.</li> </ul> Please add your own results. {| class="wikitable sortable" |- ! vendor ! model ! GHz ! cores ! time/min ! binary ! revision |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Core_2_microprocessors#.22Yorkfield.22_.2845_nm.29 Core 2 Quad Q9550] | 2.83 | 4 | 1:04 | hippo | rev32 <!-- deathspud --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Core_2_microprocessors#.22Yorkfield.22_.2845_nm.29 Core 2 Quad Q9550] | 2.83 | 4 | 1:06 | hippo_p3 | rev32 <!-- deathspud --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28standard-voltage.2C_45_nm.29 Quad Core Xeon E5420] | 2.5 | 4 | 1:16 | hippo | rev35 <!-- darthtater --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28standard-voltage.2C_45_nm.29 Quad Core Xeon E5420] | 2.5 | 4 | 1:16 | hippo | rev32 <!-- darthtater --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410] | 2.33 | 4 | 1:27 | hippo | rev32 |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410] | 2.33 | 4 | 1:31 | hippo_p3 | rev32 <!-- tinman --> |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Phenom_microprocessors#.22Agena.22_.28B2_.26_B3.2C_65_nm.29 Phenom X4 9850] | 2.5 | 4 | 1:36 | hippo_p3 | rev32 <!-- greenwulf --> |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Opteron_microprocessors#Opteron_200-series_.22SledgeHammer.22_.28B3_.26_C0_.26_CG.2C_130_nm.29 Opteron 248] | 2.2 | 1 | 2:18 | hippo_p3 | rev32 <!-- gltph --> |- | Intel | Core Duo T2300 (Mac Mini) | 1.66 | 2 | 2:41 | hippo_p3 | rev32 <!-- abbondanza --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Prestonia.22_.28standard-voltage.2C_130_nm.29 Xeon 2.4] | 2.4 | 1 | 3:03 | hippo_p3 | rev26 <!-- timberwulf --> |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Athlon_XP_microprocessors#Athlon_XP_.22Palomino.22_.28Model_6.2C_180_nm.29 Athlon XP 1800+] | 1.53 | 1 | 4:30 | hippo_p3 | rev26 |} <small>(You don't ''have'' to link to the CPU wikipedia page; just put down whatever you got and even if you're unsure. If in doubt just put the output from cat /proc/cpuinfo | \ awk 'BEGIN {FS=":"}; \ /vendor_id/ {vendor=$2}; \ /model name/ {model=$2}; \ /cpu MHz/ {GHz=$2/1000}; \ /siblings/ {cores=$2}; \ END {printf("|-\n| %s\n| %s\n| %.1f\n| %d\n| TIME\n| ?\n| ?\n", vendor, model, GHz, cores)}' into the wiki table and replace ''TIME'' by what you measured.</small> == Scaling == All tests were run with Hippo beta rev35 on empty systems. See remarks on the [[Talk:Performance#Scaling|test methodology]]. {| class="wikitable sortable" ! vendor ! # cpus or cores ! walltime and scaling |- | Intel | 4 | [[Image:Scaling Q9550.png|thumb|none|Intel Quad Core Q9550 2.8 GHz]] |- | Intel | 8 | [[Image:Scaling E5420.png|thumb|none|Dual Intel Quad Core Xeon E5420 2.5 GHz]] |- | AMD | 4 | [[Image:Scaling AMD X4 9840.png|thumb|none|AMD Phenom X4 9850 Quad Core 2.5 GHz]] |} fa08938728bdc94beb4f340088eee4b301460ad8 200 199 2008-12-08T10:23:26Z Oliver 2 /* Scaling */ wikitext text/x-wiki == Single processor performance == As a basic performance test we run the simulations in the <tt>test</tt> directory with these commands (on Linux): cd testjobs time ./calc_testjobs <ul> <li>We report the ''user'' time.</li> <li>CPU properties are found with <pre>cat /proc/cpuinfo</pre> and model names from [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors List of Intelmicroprocessors] for Intel (also see the [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors#Detailed_x86_architecture_microprocessor_lists detailed lists of Intel x86 CPUs]) and [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors List of AMD microprocessors] for AMD cpus (also see the [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors#Detailed_microprocessor_release_lists detailed lists of AMD CPUs]).</li> <li>Also report the binary used (<tt>hippo</tt> or <tt>hippo_p3</tt>) and the revision.</li> <li>Note that these tests only utilize a ''single core''.</li> <li>These results only give a rough idea of the ''relative'' performance of different architectures.</li> </ul> Please add your own results. {| class="wikitable sortable" |- ! vendor ! model ! GHz ! cores ! time/min ! binary ! revision |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Core_2_microprocessors#.22Yorkfield.22_.2845_nm.29 Core 2 Quad Q9550] | 2.83 | 4 | 1:04 | hippo | rev32 <!-- deathspud --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Core_2_microprocessors#.22Yorkfield.22_.2845_nm.29 Core 2 Quad Q9550] | 2.83 | 4 | 1:06 | hippo_p3 | rev32 <!-- deathspud --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28standard-voltage.2C_45_nm.29 Quad Core Xeon E5420] | 2.5 | 4 | 1:16 | hippo | rev35 <!-- darthtater --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28standard-voltage.2C_45_nm.29 Quad Core Xeon E5420] | 2.5 | 4 | 1:16 | hippo | rev32 <!-- darthtater --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410] | 2.33 | 4 | 1:27 | hippo | rev32 |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410] | 2.33 | 4 | 1:31 | hippo_p3 | rev32 <!-- tinman --> |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Phenom_microprocessors#.22Agena.22_.28B2_.26_B3.2C_65_nm.29 Phenom X4 9850] | 2.5 | 4 | 1:36 | hippo_p3 | rev32 <!-- greenwulf --> |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Opteron_microprocessors#Opteron_200-series_.22SledgeHammer.22_.28B3_.26_C0_.26_CG.2C_130_nm.29 Opteron 248] | 2.2 | 1 | 2:18 | hippo_p3 | rev32 <!-- gltph --> |- | Intel | Core Duo T2300 (Mac Mini) | 1.66 | 2 | 2:41 | hippo_p3 | rev32 <!-- abbondanza --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Prestonia.22_.28standard-voltage.2C_130_nm.29 Xeon 2.4] | 2.4 | 1 | 3:03 | hippo_p3 | rev26 <!-- timberwulf --> |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Athlon_XP_microprocessors#Athlon_XP_.22Palomino.22_.28Model_6.2C_180_nm.29 Athlon XP 1800+] | 1.53 | 1 | 4:30 | hippo_p3 | rev26 |} <small>(You don't ''have'' to link to the CPU wikipedia page; just put down whatever you got and even if you're unsure. If in doubt just put the output from cat /proc/cpuinfo | \ awk 'BEGIN {FS=":"}; \ /vendor_id/ {vendor=$2}; \ /model name/ {model=$2}; \ /cpu MHz/ {GHz=$2/1000}; \ /siblings/ {cores=$2}; \ END {printf("|-\n| %s\n| %s\n| %.1f\n| %d\n| TIME\n| ?\n| ?\n", vendor, model, GHz, cores)}' into the wiki table and replace ''TIME'' by what you measured.</small> == Scaling == All tests were run with Hippo beta rev35 on empty systems. See remarks on the [[Talk:Performance#Scaling|test methodology]]. In the table below, '''# cpus''' really means how many independent cores are available. {| class="wikitable sortable" |+ Scaling of the Hippo WALP test case using OpenMP on single-board machines ! vendor ! # cpus ! walltime and scaling |- | Intel | 4 | [[Image:Scaling Q9550.png|thumb|none|Intel Quad Core Q9550 2.8 GHz]] |- | Intel | 8 | [[Image:Scaling E5420.png|thumb|none|Dual Intel Quad Core Xeon E5420 2.5 GHz]] |- | AMD | 4 | [[Image:Scaling AMD X4 9840.png|thumb|none|AMD Phenom X4 9850 Quad Core 2.5 GHz]] |} 7f61a3c1954c40c8b7a1c938c9a1eed39ba8dca5 1 51 155 2008-11-14T16:03:23Z Oliver 2 automatic benchmark in distribution? wikitext text/x-wiki == Integration with tests == We could write a script that does the benchmark while running the test. It would even be possible to automatically post it (with the user's consent, of course). &mdash; [[User:Oliver|Oli]] 16:03, 14 November 2008 (UTC) d648f9fb0c92bd81affc605621f0d4317268901b 177 155 2008-12-07T13:38:51Z Oliver 2 benchmarking scaling wikitext text/x-wiki == Integration with tests == We could write a script that does the benchmark while running the test. It would even be possible to automatically post it (with the user's consent, of course). &mdash; [[User:Oliver|Oli]] 16:03, 14 November 2008 (UTC) == Scaling == Use updated [[calc_testjobs_linux.sh]] for NSLOTS in `seq 8`; do echo "-- NSLOTS = $NSLOTS"; ../../calc_testjobs_linux.sh -n $NSLOTS walp_octane_NPT_sp_MD \ | awk '/BENCHMARK/ {print $3, $4}' >> scaling.dat; done Note: * only run this on an empty machine: we are using ''wall time'' for timing ba945dfdad46e09406e1bd1e08ec88e18d1431e5 178 177 2008-12-07T13:41:02Z Oliver 2 /* Scaling */ wikitext text/x-wiki == Integration with tests == We could write a script that does the benchmark while running the test. It would even be possible to automatically post it (with the user's consent, of course). &mdash; [[User:Oliver|Oli]] 16:03, 14 November 2008 (UTC) == Scaling == Use updated [[calc_testjobs_linux.sh]] DATA=scaling.xvg echo -e "# scaling for Hippo\n# numthreads walltime/s" > $DATA for NSLOTS in `seq 8`; do echo "-- NSLOTS = $NSLOTS"; ../../calc_testjobs_linux.sh -n $NSLOTS walp_octane_NPT_sp_MD \ | awk '/BENCHMARK/ {print $3, $4}' >> $DATA; done Note: * only run this on an empty machine: we are using ''wall time'' for timing e3c02bca276782598f8a6adb87ab4f72e44ffbe2 179 178 2008-12-07T15:23:25Z Oliver 2 /* Scaling */ wikitext text/x-wiki == Integration with tests == We could write a script that does the benchmark while running the test. It would even be possible to automatically post it (with the user's consent, of course). &mdash; [[User:Oliver|Oli]] 16:03, 14 November 2008 (UTC) == Scaling == Use updated [[calc_testjobs_linux.sh]] DATA=scaling.xvg echo -e "# scaling for Hippo\n# numthreads walltime/s" > $DATA for NSLOTS in `seq 8`; do echo "-- NSLOTS = $NSLOTS"; ../../calc_testjobs_linux.sh -n $NSLOTS walp_octane_NPT_sp_MD \ | awk '/BENCHMARK/ {print $3, $4}' >> $DATA; done Note: * only run this on an empty machine: we are using ''wall time'' for timing Slightly more sophisticated: use [[test_scaling.py]]. cd testjobs test_scaling.py ''NSLOTS'' where ''NSLOTS'' is the maximum number of available cpus/cores. Results are the files scaling.xvg # numbers scaling.png # graphs 48709c96c0283da6e78cf3a6e44afd1188f88886 187 179 2008-12-07T15:41:53Z Oliver 2 /* Scaling */ wikitext text/x-wiki == Integration with tests == We could write a script that does the benchmark while running the test. It would even be possible to automatically post it (with the user's consent, of course). &mdash; [[User:Oliver|Oli]] 16:03, 14 November 2008 (UTC) == Scaling == How to run scaling tests/testing methodology: Use [[test_scaling.py]] which in turn uses [[calc_testjobs_linux.sh]]. cd testjobs test_scaling.py ''NSLOTS'' where ''NSLOTS'' is the maximum number of available cpus/cores. Results are the files scaling.xvg # numbers scaling.png # graphs * Only measures ''wall time'', hence must be run on an empty machine. * Uses <code>date +%s</code> so accuracy is limited to seconds. * No repeat runs; results may vary slightly. Manually: Use updated [[calc_testjobs_linux.sh]] DATA=scaling.xvg MAXSLOTS=8 echo -e "# scaling for Hippo\n# numthreads walltime/s" > $DATA for NSLOTS in `seq $MAXSLOTS`; do echo "-- NSLOTS = $NSLOTS"; ../../calc_testjobs_linux.sh -n $NSLOTS walp_octane_NPT_sp_MD \ | awk '/BENCHMARK/ {print $3, $4}' >> $DATA; done All the above remarks apply here, too. 4064d3553ce6ba5c739a4ff8119a289da83386b2 0 1 156 143 2008-11-14T19:35:50Z Oliver 2 /* Hippo */ wikitext text/x-wiki <div id="hauptseite"> {| width="100%" cellspacing="0" cellpadding="0" | colspan="2" | This Wiki discusses biomolecular simulations with '''[[Hippo]]''' and other molecular dynamics/Monte Carlo codes. It serves as a repository for the community and complements the [http://forums.biowerkzeug.org forums]. Please contribute your own knowledge to this Wiki: If anything is unclear and you know how to write it better – change it. If you have useful tips & tricks – share them with everyone else. If you have comments on any article in this Wiki – start a discussion on the ''discussion'' page that accompanies every article (look in the top menu bar). We only ask you to [[Special:Userlogin|register]] when you edit pages. See [[Help:Editing|Help&rarr;Editing]] to get started on contributing to this community resource. Follow the links below, use the search on the left, or browse articles by [[Special:Categories|category]]. |- | width="50%" style="vertical-align:top;" | <div id="Hippo" class="hauptseite-links"> == Hippo == <div class="inhalt"> [[Image:Hippopotamus.jpg|thumb|right|Not this hippo.]] * [[Hippo|Features]] * [[Download]] * [[Simulations]] * [[Analysis]] * [[Graphical interface]] * [[Files]] * [[Performance]] </div> </div> <div id="Methods" class="hauptseite-links"> == Methods == <div class="inhalt"> * [[Molecular dynamics]] * [[Monte Carlo]] * [[Force fields]] * [[Algorithms]] * [[Solvents]] * [[Membranes]] </div> </div> | width="50%" style="vertical-align:top;" | <div id="Simulation protocols" class="hauptseite-rechts"> == Simulation protocols == <div class="inhalt"> * [[Globular proteins]] in solvent * [[Membrane proteins]] in membrane and solvent * [[Free energy calculations]] * [[Transition path sampling]] </div> </div> <div id="Visualization" class="hauptseite-rechts"> == Visualization == <div class="inhalt"> * [[Visualization software|Software]] * [[Visualization tutorial|tutorial]] with [[VMD]] * [[Movie tutorial]] </div> </div> <div id="Software" class="hauptseite-rechts"> == Software == <div class="inhalt"> * [[Molecular dynamics codes]] * [[Monte Carlo codes]] * [[Electrostatics]] and [[Brownian dynamics]] * [[Model building]] * [[Visualization software|Visualization]] * [[Analysis software]] </div> </div> |} </div> __NOTOC__ d386149e5714b23b30794df6944bd63f6daf2e8a 165 156 2008-11-18T15:08:47Z Kaihsu 10 wikitext text/x-wiki <div id="hauptseite"> {| width="100%" cellspacing="0" cellpadding="0" | colspan="2" | This Wiki discusses biomolecular simulations with '''[[Hippo]]''' and other molecular dynamics/Monte Carlo codes. It serves as a repository for the community and complements the [http://forums.biowerkzeug.org forums]. Please contribute your own knowledge to this Wiki: If anything is unclear and you know how to write it better – change it. If you have useful tips and tricks – share them with everyone else. If you have comments on any article in this Wiki – start a discussion on the ''discussion'' page that accompanies every article (look in the top menu bar). We only ask you to [[Special:Userlogin|register]] when you edit pages. See [[Help:Editing|Help&rarr;Editing]] to get started on contributing to this community resource. Follow the links below, use the search on the left, or browse articles by [[Special:Categories|category]]. |- | width="50%" style="vertical-align:top;" | <div id="Hippo" class="hauptseite-links"> == Hippo == <div class="inhalt"> [[Image:Hippopotamus.jpg|thumb|right|Not this hippo.]] * [[Hippo|Features]] * [[Download]] * [[Simulations]] * [[Analysis]] * [[Graphical interface]] * [[Files]] * [[Performance]] </div> </div> <div id="Methods" class="hauptseite-links"> == Methods == <div class="inhalt"> * [[Molecular dynamics]] * [[Monte Carlo]] * [[Force fields]] * [[Algorithms]] * [[Solvents]] * [[Membranes]] </div> </div> | width="50%" style="vertical-align:top;" | <div id="Simulation protocols" class="hauptseite-rechts"> == Simulation protocols == <div class="inhalt"> * [[Globular proteins]] in solvent * [[Membrane proteins]] in membrane and solvent * [[Free energy calculations]] * [[Transition path sampling]] </div> </div> <div id="Visualization" class="hauptseite-rechts"> == Visualization == <div class="inhalt"> * [[Visualization software|Software]] * [[Visualization tutorial|tutorial]] with [[VMD]] * [[Movie tutorial]] </div> </div> <div id="Software" class="hauptseite-rechts"> == Software == <div class="inhalt"> * [[Molecular dynamics codes]] * [[Monte Carlo codes]] * [[Electrostatics]] and [[Brownian dynamics]] * [[Model building]] * [[Visualization software|Visualization]] * [[Analysis software]] </div> </div> |} </div> __NOTOC__ 47c111e48e83b416b45b12ad3efb66acf30a38bb 0 52 157 2008-11-14T19:38:24Z Oliver 2 download page wikitext text/x-wiki Binaries are publicly available from the [http://www.biowerkzeug.com/ Biowerkzeg.com download page] for '''Linux''' and '''Windows'''. Note that by downloading you consent to the the [[Hippo license|license]]. [[Hippo#Installing_the_software Installation of Hippo]] is trivial because the program comes as a precompiled executable and only requires a few additional data files. f5c1710c1338d18c6c72459540450c7a9c6acef5 158 157 2008-11-14T19:38:41Z Oliver 2 wikitext text/x-wiki Binaries are publicly available from the [http://www.biowerkzeug.com/ Biowerkzeg.com download page] for '''Linux''' and '''Windows'''. Note that by downloading you consent to the the [[Hippo license|license]]. [[Hippo#Installing_the_software|Installation of Hippo]] is trivial because the program comes as a precompiled executable and only requires a few additional data files. a3bc8b6b49f3c682d2dbba6917657e4cbc95e9d6 164 158 2008-11-17T16:49:00Z Kaihsu 10 correct misspelling wikitext text/x-wiki Binaries are publicly available from the [http://www.biowerkzeug.com/ Biowerkzeug.com download page] for '''Linux''' and '''Windows'''. Note that by downloading you consent to the the [[Hippo license|license]]. [[Hippo#Installing_the_software|Installation of Hippo]] is trivial because the program comes as a precompiled executable and only requires a few additional data files. 5808838d97282fdca23ba9668a88ea5c9e0a94d2 1 53 163 2008-11-17T16:48:12Z Kaihsu 10 New page: Is this a ''sui generis'' licence or is it one of the boilerplate free-software licence? Cheers. &ndash; ~~~~ wikitext text/x-wiki Is this a ''sui generis'' licence or is it one of the boilerplate free-software licence? Cheers. &ndash; [[User:Kaihsu|Kaihsu]] 16:48, 17 November 2008 (UTC) 14d1cabdd6a456cfe5345e6710e9a46fbca194b5 0 54 176 2008-12-07T13:37:17Z Oliver 2 benchmarking and testing script wikitext text/x-wiki This script allows running Hippo benchmarks. <pre>#!/bin/bash # Running Hippo tests (Linux) # Copyright (c) 2008 Biowerkzeug # Oliver Beckstein <orbeckst@gmail.com> #set -x prog=$(basename $0) CURDIR=${PWD} # defaults (: can be set in environment) : ${HIPPO_DIR:="${CURDIR}/.."} HIPPO_TESTS="hexane_NVT_dp_MD octane_NPT_sp_MC pentadecane_NPT_sp_MD tip3p_NPT_sp_MD trpzip2_GBSA_MC vpu_GBIM_MC walp_octane_NPT_sp_MD" RUN_TESTS=${HIPPO_TESTS} USE_MPI=0 usage="usage $prog [opts] [tests] Run Hippo tests. By default it runs all of them: ${HIPPO_TESTS} OPTIONS: -h help -n number of threads (not possible for all tests) -D directory where we look for Hippo executables [${HIPPO_DIR}] -M use mpi (replica exchange) binaries [${USE_MPI}] Environment variables: HIPPO_DIR overrides -D [${HIPPO_DIR}] " function die () { local msg="$1" err=${2:-1} echo 1>&2 "ERROR: failed in $PWD: ${msg}" cd ${CURDIR} exit $err } NSLOTS=1 # opt processing while getopts hn:D:M: opt; do case $opt in h) echo "$usage"; exit 0;; n) NSLOTS=${OPTARG};; D) HIPPO_DIR=${OPTARG};; M) USE_MPI=${OPTARG};; *) die "Unknown option" 1;; esac done #echo "OPTIND=$OPTIND OPTARG=$OPTARG argv=$*" shift $((OPTIND - 1)) if [ -n "$*" ]; then RUN_TESTS="$*" fi echo "Running the following tests using ${NSLOTS} threads: ${RUN_TESTS}" # find working executable # we'll use the first one that only complain about missing input file # if [ ${USE_MPI} = 0 ]; then echo "Only trying single cpu binaries" _HIPPO_BINARIES="hippo hippo_p3" else _HIPPO_BINARIES="hippo_mpi hippo hippo_p3_mpi hippo_p3" fi HIPPO="not_found" rm -f hippo_input.txt # clean any input files for h in ${_HIPPO_BINARIES}; do exe="${HIPPO_DIR}/${h}" if ${exe} 2>&1 | egrep "^Hippo.*Copyright.*Biowerkzeug" >/dev/null; then HIPPO=${exe} break fi done if [ "${HIPPO}" = "not_found" ]; then ARCH=$(uname -m); OS=$(uname -s); die "No usable hippo executable found; see if there is one at http://www.biowerkzeug.com for your architecture ${ARCH} and operating system ${OS}. " fi echo "Using executable ${HIPPO}" TOPOLOGY=${HIPPO_DIR}/hippo_protein_database.dat FF=${HIPPO_DIR}/oplsaa_forcefield.dat echo "Setting up test directory" rm -rf test mkdir test cd test topdir="${CURDIR}/test" function setup_hippo () { local numthreads=${1:-1} local input=hippo_input.txt cp ${HIPPO} ./hippo || return $? cp ${TOPOLOGY} . || return $? cp ${FF} . || return $? test -e $input || die "Missing run input file $input in $PWD" if [ $NSLOTS -gt 1 ]; then # adjusting for OpenMP run sed -i.orig -e "s/[[:space:]]*openMP numthreads.*/openMP numthreads ${numthreads}/" $input fi return 0 } function run_test () { local testdir="$1" numthreads="${2:-1}" echo "---------------------------------------------------------" cd ${testdir} || die "Cannot 'cd ${testdir}'" setup_hippo ${numthreads} || die "setup_hippo() failed" echo "Set up all files for NSLOTS=${numthreads}" echo "Running hippo test case ${testdir}..." t_start=$(date +%s) ./hippo t_stop=$(date +%s) delta_t=$(( t_stop-t_start )) echo "Completed hippo test case ${testdir} in ${delta_t} seconds, running ${numthreads} threads" echo "BENCHMARK: ${testdir} ${numthreads} ${delta_t}" cd ${topdir} } cp -r ../jobs/* . for t in ${RUN_TESTS}; do run_test $t ${NSLOTS} done echo "Finished running hippo test suite" </pre> ba873fc7df617b505a6bfb2ed8ad7ee25c80dd61 191 176 2008-12-07T16:03:47Z Oliver 2 wikitext text/x-wiki This script allows running Hippo benchmarks without having to think too much about finding the correct binary and supplemental files. In addition it gives the total wall time required to run each test case; this can be used for crude benchmarks. <pre>#!/bin/bash # Running Hippo tests (Linux) # Copyright (c) 2008 Biowerkzeug # Oliver Beckstein <orbeckst@gmail.com> #set -x prog=$(basename $0) CURDIR=${PWD} # defaults (: can be set in environment) : ${HIPPO_DIR:="${CURDIR}/.."} HIPPO_TESTS="hexane_NVT_dp_MD octane_NPT_sp_MC pentadecane_NPT_sp_MD tip3p_NPT_sp_MD trpzip2_GBSA_MC vpu_GBIM_MC walp_octane_NPT_sp_MD" RUN_TESTS=${HIPPO_TESTS} USE_MPI=0 usage="usage $prog [opts] [tests] Run Hippo tests. By default it runs all of them: ${HIPPO_TESTS} OPTIONS: -h help -n number of threads (not possible for all tests) -D directory where we look for Hippo executables [${HIPPO_DIR}] -M use mpi (replica exchange) binaries [${USE_MPI}] Environment variables: HIPPO_DIR overrides -D [${HIPPO_DIR}] " function die () { local msg="$1" err=${2:-1} echo 1>&2 "ERROR: failed in $PWD: ${msg}" cd ${CURDIR} exit $err } NSLOTS=1 # opt processing while getopts hn:D:M: opt; do case $opt in h) echo "$usage"; exit 0;; n) NSLOTS=${OPTARG};; D) HIPPO_DIR=${OPTARG};; M) USE_MPI=${OPTARG};; *) die "Unknown option" 1;; esac done #echo "OPTIND=$OPTIND OPTARG=$OPTARG argv=$*" shift $((OPTIND - 1)) if [ -n "$*" ]; then RUN_TESTS="$*" fi echo "Running the following tests using ${NSLOTS} threads: ${RUN_TESTS}" # find working executable # we'll use the first one that only complain about missing input file # if [ ${USE_MPI} = 0 ]; then echo "Only trying single cpu binaries" _HIPPO_BINARIES="hippo hippo_p3" else _HIPPO_BINARIES="hippo_mpi hippo hippo_p3_mpi hippo_p3" fi HIPPO="not_found" rm -f hippo_input.txt # clean any input files for h in ${_HIPPO_BINARIES}; do exe="${HIPPO_DIR}/${h}" if ${exe} 2>&1 | egrep "^Hippo.*Copyright.*Biowerkzeug" >/dev/null; then HIPPO=${exe} break fi done if [ "${HIPPO}" = "not_found" ]; then ARCH=$(uname -m); OS=$(uname -s); die "No usable hippo executable found; see if there is one at http://www.biowerkzeug.com for your architecture ${ARCH} and operating system ${OS}. " fi echo "Using executable ${HIPPO}" TOPOLOGY=${HIPPO_DIR}/hippo_protein_database.dat FF=${HIPPO_DIR}/oplsaa_forcefield.dat echo "Setting up test directory" rm -rf test mkdir test cd test topdir="${CURDIR}/test" function setup_hippo () { local numthreads=${1:-1} local input=hippo_input.txt cp ${HIPPO} ./hippo || return $? cp ${TOPOLOGY} . || return $? cp ${FF} . || return $? test -e $input || die "Missing run input file $input in $PWD" if [ $NSLOTS -gt 1 ]; then # adjusting for OpenMP run sed -i.orig -e "s/[[:space:]]*openMP numthreads.*/openMP numthreads ${numthreads}/" $input fi return 0 } function run_test () { local testdir="$1" numthreads="${2:-1}" echo "---------------------------------------------------------" cd ${testdir} || die "Cannot 'cd ${testdir}'" setup_hippo ${numthreads} || die "setup_hippo() failed" echo "Set up all files for NSLOTS=${numthreads}" echo "Running hippo test case ${testdir}..." t_start=$(date +%s) ./hippo t_stop=$(date +%s) delta_t=$(( t_stop-t_start )) echo "Completed hippo test case ${testdir} in ${delta_t} seconds, running ${numthreads} threads" echo "BENCHMARK: ${testdir} ${numthreads} ${delta_t}" cd ${topdir} } cp -r ../jobs/* . for t in ${RUN_TESTS}; do run_test $t ${NSLOTS} done echo "Finished running hippo test suite" </pre> 8d22b79ff8d72fdf68bbc850a4f74e65c452b065 192 191 2008-12-07T16:08:31Z Oliver 2 calc_testjobs_linux.sh 2535 2008-12-07 16:07:19Z wikitext text/x-wiki This script allows running Hippo benchmarks without having to think too much about finding the correct binary and supplemental files. In addition it gives the total wall time required to run each test case; this can be used for crude benchmarks. <pre>#!/bin/bash # $Id: calc_testjobs_linux.sh 2535 2008-12-07 16:07:19Z www-data $ # Running Hippo tests (Linux) # Copyright (c) 2008 Biowerkzeug # Oliver Beckstein <orbeckst@gmail.com> #set -x prog=$(basename $0) CURDIR=${PWD} # defaults (: can be set in environment) : ${HIPPO_DIR:="${CURDIR}/.."} HIPPO_TESTS="hexane_NVT_dp_MD octane_NPT_sp_MC pentadecane_NPT_sp_MD tip3p_NPT_sp_MD trpzip2_GBSA_MC vpu_GBIM_MC walp_octane_NPT_sp_MD" RUN_TESTS=${HIPPO_TESTS} USE_MPI=0 usage="usage $prog [opts] [tests] Run Hippo tests. By default it runs all of them: ${HIPPO_TESTS} OPTIONS: -h help -n number of threads (not possible for all tests) -D directory where we look for Hippo executables [${HIPPO_DIR}] -M use mpi (replica exchange) binaries [${USE_MPI}] Environment variables: HIPPO_DIR overrides -D [${HIPPO_DIR}] " function die () { local msg="$1" err=${2:-1} echo 1>&2 "ERROR: failed in $PWD: ${msg}" cd ${CURDIR} exit $err } NSLOTS=1 # opt processing while getopts hn:D:M: opt; do case $opt in h) echo "$usage"; exit 0;; n) NSLOTS=${OPTARG};; D) HIPPO_DIR=${OPTARG};; M) USE_MPI=${OPTARG};; *) die "Unknown option" 1;; esac done #echo "OPTIND=$OPTIND OPTARG=$OPTARG argv=$*" shift $((OPTIND - 1)) if [ -n "$*" ]; then RUN_TESTS="$*" fi echo "Running the following tests using ${NSLOTS} threads: ${RUN_TESTS}" # find working executable # we'll use the first one that only complain about missing input file # if [ ${USE_MPI} = 0 ]; then echo "Trying standard binaries (with OpenMP)" _HIPPO_BINARIES="hippo hippo_p3" else echo "Testing mpi binaries. Note: these are ONLY needed for replica exchange simulations" _HIPPO_BINARIES="hippo_mpi hippo_p3_mpi" fi HIPPO="not_found" rm -f hippo_input.txt # clean any input files for h in ${_HIPPO_BINARIES}; do exe="${HIPPO_DIR}/${h}" if ${exe} 2>&1 | egrep "^Hippo.*Copyright.*Biowerkzeug" >/dev/null; then HIPPO=${exe} break fi done if [ "${HIPPO}" = "not_found" ]; then ARCH=$(uname -m); OS=$(uname -s); die "No usable hippo executable found; see if there is one at http://www.biowerkzeug.com for your architecture ${ARCH} and operating system ${OS}. " fi echo "Using executable ${HIPPO}" TOPOLOGY=${HIPPO_DIR}/hippo_protein_database.dat FF=${HIPPO_DIR}/oplsaa_forcefield.dat echo "Setting up test directory" rm -rf test mkdir test cd test topdir="${CURDIR}/test" function setup_hippo () { local numthreads=${1:-1} local input=hippo_input.txt cp ${HIPPO} ./hippo || return $? cp ${TOPOLOGY} . || return $? cp ${FF} . || return $? test -e $input || die "Missing run input file $input in $PWD" if [ $NSLOTS -gt 1 ]; then # adjusting for OpenMP run sed -i.orig -e "s/[[:space:]]*openMP numthreads.*/openMP numthreads ${numthreads}/" $input fi return 0 } function run_test () { local testdir="$1" numthreads="${2:-1}" echo "---------------------------------------------------------" cd ${testdir} || die "Cannot 'cd ${testdir}'" setup_hippo ${numthreads} || die "setup_hippo() failed" echo "Set up all files for NSLOTS=${numthreads}" echo "Running hippo test case ${testdir}..." t_start=$(date +%s) ./hippo t_stop=$(date +%s) delta_t=$(( t_stop-t_start )) echo "Completed hippo test case ${testdir} in ${delta_t} seconds, running ${numthreads} threads" echo "BENCHMARK: ${testdir} ${numthreads} ${delta_t}" cd ${topdir} } cp -r ../jobs/* . for t in ${RUN_TESTS}; do run_test $t ${NSLOTS} done echo "Finished running hippo test suite" </pre> 85a1a1317ef84db3871fd481c1aeaa4fc2b7b9b8 193 192 2008-12-07T16:12:54Z Oliver 2 no mpi wikitext text/x-wiki This script allows running Hippo benchmarks without having to think too much about finding the correct binary and supplemental files. In addition it gives the total wall time required to run each test case; this can be used for crude benchmarks. * The testing of the mpi binaries is not tested and probably does not work. However, they are ''only'' needed for replica exchange simulations and there are no test cases for those anyway. * [http://forums.biowerkzeug.org/viewtopic.php?f=22&t=6&p=15&hilit=OpenMP#p15 Not all tests support multi-threaded runs] (with OpneMP); these tests ignore the NSLOTS argument. <pre>#!/bin/bash # $Id: calc_testjobs_linux.sh 2535 2008-12-07 16:07:19Z www-data $ # Running Hippo tests (Linux) # Copyright (c) 2008 Biowerkzeug # Oliver Beckstein <orbeckst@gmail.com> #set -x prog=$(basename $0) CURDIR=${PWD} # defaults (: can be set in environment) : ${HIPPO_DIR:="${CURDIR}/.."} HIPPO_TESTS="hexane_NVT_dp_MD octane_NPT_sp_MC pentadecane_NPT_sp_MD tip3p_NPT_sp_MD trpzip2_GBSA_MC vpu_GBIM_MC walp_octane_NPT_sp_MD" RUN_TESTS=${HIPPO_TESTS} USE_MPI=0 usage="usage $prog [opts] [tests] Run Hippo tests. By default it runs all of them: ${HIPPO_TESTS} OPTIONS: -h help -n number of threads (not possible for all tests) -D directory where we look for Hippo executables [${HIPPO_DIR}] -M use mpi (replica exchange) binaries [${USE_MPI}] Environment variables: HIPPO_DIR overrides -D [${HIPPO_DIR}] " function die () { local msg="$1" err=${2:-1} echo 1>&2 "ERROR: failed in $PWD: ${msg}" cd ${CURDIR} exit $err } NSLOTS=1 # opt processing while getopts hn:D:M: opt; do case $opt in h) echo "$usage"; exit 0;; n) NSLOTS=${OPTARG};; D) HIPPO_DIR=${OPTARG};; M) USE_MPI=${OPTARG};; *) die "Unknown option" 1;; esac done #echo "OPTIND=$OPTIND OPTARG=$OPTARG argv=$*" shift $((OPTIND - 1)) if [ -n "$*" ]; then RUN_TESTS="$*" fi echo "Running the following tests using ${NSLOTS} threads: ${RUN_TESTS}" # find working executable # we'll use the first one that only complain about missing input file # if [ ${USE_MPI} = 0 ]; then echo "Trying standard binaries (with OpenMP)" _HIPPO_BINARIES="hippo hippo_p3" else echo "Testing mpi binaries. Note: these are ONLY needed for replica exchange simulations" _HIPPO_BINARIES="hippo_mpi hippo_p3_mpi" fi HIPPO="not_found" rm -f hippo_input.txt # clean any input files for h in ${_HIPPO_BINARIES}; do exe="${HIPPO_DIR}/${h}" if ${exe} 2>&1 | egrep "^Hippo.*Copyright.*Biowerkzeug" >/dev/null; then HIPPO=${exe} break fi done if [ "${HIPPO}" = "not_found" ]; then ARCH=$(uname -m); OS=$(uname -s); die "No usable hippo executable found; see if there is one at http://www.biowerkzeug.com for your architecture ${ARCH} and operating system ${OS}. " fi echo "Using executable ${HIPPO}" TOPOLOGY=${HIPPO_DIR}/hippo_protein_database.dat FF=${HIPPO_DIR}/oplsaa_forcefield.dat echo "Setting up test directory" rm -rf test mkdir test cd test topdir="${CURDIR}/test" function setup_hippo () { local numthreads=${1:-1} local input=hippo_input.txt cp ${HIPPO} ./hippo || return $? cp ${TOPOLOGY} . || return $? cp ${FF} . || return $? test -e $input || die "Missing run input file $input in $PWD" if [ $NSLOTS -gt 1 ]; then # adjusting for OpenMP run sed -i.orig -e "s/[[:space:]]*openMP numthreads.*/openMP numthreads ${numthreads}/" $input fi return 0 } function run_test () { local testdir="$1" numthreads="${2:-1}" echo "---------------------------------------------------------" cd ${testdir} || die "Cannot 'cd ${testdir}'" setup_hippo ${numthreads} || die "setup_hippo() failed" echo "Set up all files for NSLOTS=${numthreads}" echo "Running hippo test case ${testdir}..." t_start=$(date +%s) ./hippo t_stop=$(date +%s) delta_t=$(( t_stop-t_start )) echo "Completed hippo test case ${testdir} in ${delta_t} seconds, running ${numthreads} threads" echo "BENCHMARK: ${testdir} ${numthreads} ${delta_t}" cd ${topdir} } cp -r ../jobs/* . for t in ${RUN_TESTS}; do run_test $t ${NSLOTS} done echo "Finished running hippo test suite" </pre> c9c3a3d2964cc86f5e5f4c3259d6aa98b97b8a63 194 193 2008-12-07T16:13:14Z Oliver 2 wikitext text/x-wiki This script allows running Hippo benchmarks without having to think too much about finding the correct binary and supplemental files. In addition it gives the total wall time required to run each test case; this can be used for crude benchmarks. * The testing of the mpi binaries is not tested and probably does not work. However, they are ''only'' needed for replica exchange simulations and there are no test cases for those anyway. * [http://forums.biowerkzeug.org/viewtopic.php?f=22&t=6&p=15&hilit=OpenMP#p15 Not all tests support multi-threaded runs] (with Opn)n; these tests ignore the NSLOTS argument. <pre>#!/bin/bash # $Id: calc_testjobs_linux.sh 2535 2008-12-07 16:07:19Z www-data $ # Running Hippo tests (Linux) # Copyright (c) 2008 Biowerkzeug # Oliver Beckstein <orbeckst@gmail.com> #set -x prog=$(basename $0) CURDIR=${PWD} # defaults (: can be set in environment) : ${HIPPO_DIR:="${CURDIR}/.."} HIPPO_TESTS="hexane_NVT_dp_MD octane_NPT_sp_MC pentadecane_NPT_sp_MD tip3p_NPT_sp_MD trpzip2_GBSA_MC vpu_GBIM_MC walp_octane_NPT_sp_MD" RUN_TESTS=${HIPPO_TESTS} USE_MPI=0 usage="usage $prog [opts] [tests] Run Hippo tests. By default it runs all of them: ${HIPPO_TESTS} OPTIONS: -h help -n number of threads (not possible for all tests) -D directory where we look for Hippo executables [${HIPPO_DIR}] -M use mpi (replica exchange) binaries [${USE_MPI}] Environment variables: HIPPO_DIR overrides -D [${HIPPO_DIR}] " function die () { local msg="$1" err=${2:-1} echo 1>&2 "ERROR: failed in $PWD: ${msg}" cd ${CURDIR} exit $err } NSLOTS=1 # opt processing while getopts hn:D:M: opt; do case $opt in h) echo "$usage"; exit 0;; n) NSLOTS=${OPTARG};; D) HIPPO_DIR=${OPTARG};; M) USE_MPI=${OPTARG};; *) die "Unknown option" 1;; esac done #echo "OPTIND=$OPTIND OPTARG=$OPTARG argv=$*" shift $((OPTIND - 1)) if [ -n "$*" ]; then RUN_TESTS="$*" fi echo "Running the following tests using ${NSLOTS} threads: ${RUN_TESTS}" # find working executable # we'll use the first one that only complain about missing input file # if [ ${USE_MPI} = 0 ]; then echo "Trying standard binaries (with OpenMP)" _HIPPO_BINARIES="hippo hippo_p3" else echo "Testing mpi binaries. Note: these are ONLY needed for replica exchange simulations" _HIPPO_BINARIES="hippo_mpi hippo_p3_mpi" fi HIPPO="not_found" rm -f hippo_input.txt # clean any input files for h in ${_HIPPO_BINARIES}; do exe="${HIPPO_DIR}/${h}" if ${exe} 2>&1 | egrep "^Hippo.*Copyright.*Biowerkzeug" >/dev/null; then HIPPO=${exe} break fi done if [ "${HIPPO}" = "not_found" ]; then ARCH=$(uname -m); OS=$(uname -s); die "No usable hippo executable found; see if there is one at http://www.biowerkzeug.com for your architecture ${ARCH} and operating system ${OS}. " fi echo "Using executable ${HIPPO}" TOPOLOGY=${HIPPO_DIR}/hippo_protein_database.dat FF=${HIPPO_DIR}/oplsaa_forcefield.dat echo "Setting up test directory" rm -rf test mkdir test cd test topdir="${CURDIR}/test" function setup_hippo () { local numthreads=${1:-1} local input=hippo_input.txt cp ${HIPPO} ./hippo || return $? cp ${TOPOLOGY} . || return $? cp ${FF} . || return $? test -e $input || die "Missing run input file $input in $PWD" if [ $NSLOTS -gt 1 ]; then # adjusting for OpenMP run sed -i.orig -e "s/[[:space:]]*openMP numthreads.*/openMP numthreads ${numthreads}/" $input fi return 0 } function run_test () { local testdir="$1" numthreads="${2:-1}" echo "---------------------------------------------------------" cd ${testdir} || die "Cannot 'cd ${testdir}'" setup_hippo ${numthreads} || die "setup_hippo() failed" echo "Set up all files for NSLOTS=${numthreads}" echo "Running hippo test case ${testdir}..." t_start=$(date +%s) ./hippo t_stop=$(date +%s) delta_t=$(( t_stop-t_start )) echo "Completed hippo test case ${testdir} in ${delta_t} seconds, running ${numthreads} threads" echo "BENCHMARK: ${testdir} ${numthreads} ${delta_t}" cd ${topdir} } cp -r ../jobs/* . for t in ${RUN_TESTS}; do run_test $t ${NSLOTS} done echo "Finished running hippo test suite" </pre> 5ea818a70b27b397223f2201278652ca0f3013a4 195 194 2008-12-07T16:13:33Z Oliver 2 wikitext text/x-wiki This script allows running Hippo benchmarks without having to think too much about finding the correct binary and supplemental files. In addition it gives the total wall time required to run each test case; this can be used for crude benchmarks. * The testing of the mpi binaries is not tested and probably does not work. However, they are ''only'' needed for replica exchange simulations and there are no test cases for those anyway. * [http://forums.biowerkzeug.org/viewtopic.php?f=22&t=6&p=15&hilit=OpenMP#p15 Not all tests support multi-threaded runs] (with OpenMP); these tests ignore the NSLOTS argument. <pre>#!/bin/bash # $Id: calc_testjobs_linux.sh 2535 2008-12-07 16:07:19Z www-data $ # Running Hippo tests (Linux) # Copyright (c) 2008 Biowerkzeug # Oliver Beckstein <orbeckst@gmail.com> #set -x prog=$(basename $0) CURDIR=${PWD} # defaults (: can be set in environment) : ${HIPPO_DIR:="${CURDIR}/.."} HIPPO_TESTS="hexane_NVT_dp_MD octane_NPT_sp_MC pentadecane_NPT_sp_MD tip3p_NPT_sp_MD trpzip2_GBSA_MC vpu_GBIM_MC walp_octane_NPT_sp_MD" RUN_TESTS=${HIPPO_TESTS} USE_MPI=0 usage="usage $prog [opts] [tests] Run Hippo tests. By default it runs all of them: ${HIPPO_TESTS} OPTIONS: -h help -n number of threads (not possible for all tests) -D directory where we look for Hippo executables [${HIPPO_DIR}] -M use mpi (replica exchange) binaries [${USE_MPI}] Environment variables: HIPPO_DIR overrides -D [${HIPPO_DIR}] " function die () { local msg="$1" err=${2:-1} echo 1>&2 "ERROR: failed in $PWD: ${msg}" cd ${CURDIR} exit $err } NSLOTS=1 # opt processing while getopts hn:D:M: opt; do case $opt in h) echo "$usage"; exit 0;; n) NSLOTS=${OPTARG};; D) HIPPO_DIR=${OPTARG};; M) USE_MPI=${OPTARG};; *) die "Unknown option" 1;; esac done #echo "OPTIND=$OPTIND OPTARG=$OPTARG argv=$*" shift $((OPTIND - 1)) if [ -n "$*" ]; then RUN_TESTS="$*" fi echo "Running the following tests using ${NSLOTS} threads: ${RUN_TESTS}" # find working executable # we'll use the first one that only complain about missing input file # if [ ${USE_MPI} = 0 ]; then echo "Trying standard binaries (with OpenMP)" _HIPPO_BINARIES="hippo hippo_p3" else echo "Testing mpi binaries. Note: these are ONLY needed for replica exchange simulations" _HIPPO_BINARIES="hippo_mpi hippo_p3_mpi" fi HIPPO="not_found" rm -f hippo_input.txt # clean any input files for h in ${_HIPPO_BINARIES}; do exe="${HIPPO_DIR}/${h}" if ${exe} 2>&1 | egrep "^Hippo.*Copyright.*Biowerkzeug" >/dev/null; then HIPPO=${exe} break fi done if [ "${HIPPO}" = "not_found" ]; then ARCH=$(uname -m); OS=$(uname -s); die "No usable hippo executable found; see if there is one at http://www.biowerkzeug.com for your architecture ${ARCH} and operating system ${OS}. " fi echo "Using executable ${HIPPO}" TOPOLOGY=${HIPPO_DIR}/hippo_protein_database.dat FF=${HIPPO_DIR}/oplsaa_forcefield.dat echo "Setting up test directory" rm -rf test mkdir test cd test topdir="${CURDIR}/test" function setup_hippo () { local numthreads=${1:-1} local input=hippo_input.txt cp ${HIPPO} ./hippo || return $? cp ${TOPOLOGY} . || return $? cp ${FF} . || return $? test -e $input || die "Missing run input file $input in $PWD" if [ $NSLOTS -gt 1 ]; then # adjusting for OpenMP run sed -i.orig -e "s/[[:space:]]*openMP numthreads.*/openMP numthreads ${numthreads}/" $input fi return 0 } function run_test () { local testdir="$1" numthreads="${2:-1}" echo "---------------------------------------------------------" cd ${testdir} || die "Cannot 'cd ${testdir}'" setup_hippo ${numthreads} || die "setup_hippo() failed" echo "Set up all files for NSLOTS=${numthreads}" echo "Running hippo test case ${testdir}..." t_start=$(date +%s) ./hippo t_stop=$(date +%s) delta_t=$(( t_stop-t_start )) echo "Completed hippo test case ${testdir} in ${delta_t} seconds, running ${numthreads} threads" echo "BENCHMARK: ${testdir} ${numthreads} ${delta_t}" cd ${topdir} } cp -r ../jobs/* . for t in ${RUN_TESTS}; do run_test $t ${NSLOTS} done echo "Finished running hippo test suite" </pre> 41fa8e80c0a041292f62fd66ba594c878947fcc4 0 55 180 2008-12-07T15:25:50Z Oliver 2 test_scaling.py 2533 2008-12-07 15:11:10Z wikitext text/x-wiki Python script that uses [[calc_testjobs_linux.sh]] to benchmark scaling using the ''walp_octane_NPT_sp_MD'' test case. See [[Talk:Performace#Scaling]] for details. <pre>#!/usr/bin/env python # $Id: test_scaling.py 2533 2008-12-07 15:11:10Z www-data $ # Testing scaling of hippo # Copyright (c) 2008 Biowerkzeug # Oliver Beckstein <orbeckst@gmail.com> from subprocess import Popen,PIPE import sys,re calc_test_jobs = '/home/oliver/Library/Hippo/Benchmark/calc_testjobs_linux.sh' hippo_test_case = 'walp_octane_NPT_sp_MD' filename = "scaling.xvg" figname = "scaling.png" try: maxslots = int(sys.argv[1]) except: print "usage: %s NSLOTS" % sys.argv[0] sys.exit(1) slotrange = (1,maxslots+1) # <--- 1-4 !! benchmark_pattern = re.compile(r'BENCHMARK:\s*(\w+)\s+(?P<NUMTHREADS>[0-9]+)\s+(?P<T_SECONDS>[0-9.]+)') runtime = {} out = open(filename,'w') out.write("# scaling for Hippo\n# numthreads walltime/s scaling\n") for NSLOTS in xrange(*slotrange): print "-- running NSLOTS = %(NSLOTS)d" % vars() p1 = Popen([calc_test_jobs, '-n', str(NSLOTS), hippo_test_case],stdout=PIPE) p2 = Popen(['grep','BENCHMARK:'],stdin=p1.stdout,stdout=PIPE) output = p2.communicate()[0] m = benchmark_pattern.match(output) print "output: ",output, if not m: print "ERROR: no benchmark data found" continue numthreads = int(m.group('NUMTHREADS')) walltime = float(m.group('T_SECONDS')) runtime[numthreads] = walltime scaling = walltime/runtime[1] # runtime[1] is known after the first iteration! out.write("%(numthreads)d %(walltime)f %(scaling)f\n" % vars()) out.close() # Analysis import numpy import pylab N = numpy.sort(runtime.keys()) T = numpy.array([runtime[n] for n in N],dtype=float) S = T[0]/T pylab.clf() pylab.subplot(211) pylab.title('Hippo test case: '+hippo_test_case) pylab.xlabel('cpus') pylab.ylabel('walltime/s') pylab.plot(N,T,'ro-') pylab.subplot(212) pylab.xlabel('cpus') pylab.ylabel('scaling') pylab.plot(N,S,'ro-') pylab.plot([N[0],N[-1]], [1,N[-1]], 'k--') pylab.savefig(figname) print "Saved figure "+figname </pre> 340ee51336ff602b2cef929d4f188f34ef56e6e4 181 180 2008-12-07T15:26:28Z Oliver 2 wikitext text/x-wiki Python script that uses [[calc_testjobs_linux.sh]] to benchmark scaling using the ''walp_octane_NPT_sp_MD'' test case. See [[Talk:Performance#Scaling]] for details. <pre>#!/usr/bin/env python # $Id: test_scaling.py 2533 2008-12-07 15:11:10Z www-data $ # Testing scaling of hippo # Copyright (c) 2008 Biowerkzeug # Oliver Beckstein <orbeckst@gmail.com> from subprocess import Popen,PIPE import sys,re calc_test_jobs = '/home/oliver/Library/Hippo/Benchmark/calc_testjobs_linux.sh' hippo_test_case = 'walp_octane_NPT_sp_MD' filename = "scaling.xvg" figname = "scaling.png" try: maxslots = int(sys.argv[1]) except: print "usage: %s NSLOTS" % sys.argv[0] sys.exit(1) slotrange = (1,maxslots+1) # <--- 1-4 !! benchmark_pattern = re.compile(r'BENCHMARK:\s*(\w+)\s+(?P<NUMTHREADS>[0-9]+)\s+(?P<T_SECONDS>[0-9.]+)') runtime = {} out = open(filename,'w') out.write("# scaling for Hippo\n# numthreads walltime/s scaling\n") for NSLOTS in xrange(*slotrange): print "-- running NSLOTS = %(NSLOTS)d" % vars() p1 = Popen([calc_test_jobs, '-n', str(NSLOTS), hippo_test_case],stdout=PIPE) p2 = Popen(['grep','BENCHMARK:'],stdin=p1.stdout,stdout=PIPE) output = p2.communicate()[0] m = benchmark_pattern.match(output) print "output: ",output, if not m: print "ERROR: no benchmark data found" continue numthreads = int(m.group('NUMTHREADS')) walltime = float(m.group('T_SECONDS')) runtime[numthreads] = walltime scaling = walltime/runtime[1] # runtime[1] is known after the first iteration! out.write("%(numthreads)d %(walltime)f %(scaling)f\n" % vars()) out.close() # Analysis import numpy import pylab N = numpy.sort(runtime.keys()) T = numpy.array([runtime[n] for n in N],dtype=float) S = T[0]/T pylab.clf() pylab.subplot(211) pylab.title('Hippo test case: '+hippo_test_case) pylab.xlabel('cpus') pylab.ylabel('walltime/s') pylab.plot(N,T,'ro-') pylab.subplot(212) pylab.xlabel('cpus') pylab.ylabel('scaling') pylab.plot(N,S,'ro-') pylab.plot([N[0],N[-1]], [1,N[-1]], 'k--') pylab.savefig(figname) print "Saved figure "+figname </pre> e0bb0798c8fdc3bfe67b15580e086a01b0949920 190 181 2008-12-07T16:00:51Z Oliver 2 test_scaling.py 2534 2008-12-07 15:59:59Z wikitext text/x-wiki Python script that uses [[calc_testjobs_linux.sh]] to benchmark scaling using the ''walp_octane_NPT_sp_MD'' test case. See [[Talk:Performance#Scaling]] for details. <pre>#!/usr/bin/env python # $Id: test_scaling.py 2534 2008-12-07 15:59:59Z www-data $ # Testing scaling of hippo # Copyright (c) 2008 Biowerkzeug # Oliver Beckstein <orbeckst@gmail.com> from subprocess import Popen,PIPE import sys,re calc_test_jobs = '/home/oliver/Library/Hippo/Benchmark/calc_testjobs_linux.sh' hippo_test_case = 'walp_octane_NPT_sp_MD' filename = "scaling.xvg" figname = "scaling.png" try: maxslots = int(sys.argv[1]) except: print "usage: %s NSLOTS" % sys.argv[0] sys.exit(1) slotrange = (1,maxslots+1) # <--- 1-4 !! benchmark_pattern = re.compile(r'BENCHMARK:\s*(\w+)\s+(?P<NUMTHREADS>[0-9]+)\s+(?P<T_SECONDS>[0-9.]+)') runtime = {} out = open(filename,'w') out.write("# scaling for Hippo\n# numthreads walltime/s scaling\n") for NSLOTS in xrange(*slotrange): print "-- running NSLOTS = %(NSLOTS)d" % vars() p1 = Popen([calc_test_jobs, '-n', str(NSLOTS), hippo_test_case],stdout=PIPE) p2 = Popen(['grep','BENCHMARK:'],stdin=p1.stdout,stdout=PIPE) output = p2.communicate()[0] m = benchmark_pattern.match(output) print "output: ",output, if not m: print "ERROR: no benchmark data found" continue numthreads = int(m.group('NUMTHREADS')) walltime = float(m.group('T_SECONDS')) runtime[numthreads] = walltime scaling = runtime[1]/walltime # runtime[1] is known after the first iteration! out.write("%(numthreads)d %(walltime)f %(scaling)f\n" % vars()) out.close() # Analysis import numpy import pylab N = numpy.sort(runtime.keys()) T = numpy.array([runtime[n] for n in N],dtype=float) S = T[0]/T pylab.clf() pylab.subplot(211) pylab.title('Hippo test case: '+hippo_test_case) pylab.xlabel('cpus') pylab.ylabel('walltime/s') pylab.plot(N,T,'ro-') pylab.subplot(212) pylab.xlabel('cpus') pylab.ylabel('scaling') pylab.plot(N,S,'ro-') pylab.plot([N[0],N[-1]], [1,N[-1]], 'k--') pylab.savefig(figname) print "Saved figure "+figname </pre> 9d864fe9bbafbe40e0526379b379dd92a915e919 6 56 182 2008-12-07T15:30:24Z Oliver 2 Scaling of WALP test case on Intel Q9550. Hippo rev35. wikitext text/x-wiki Scaling of WALP test case on Intel Q9550. Hippo rev35. b6ca048a5258caed8ef19f0b0a93e70c602eac72 188 182 2008-12-07T15:52:01Z Oliver 2 uploaded a new version of "[[Image:Scaling Q9550.png]]" wikitext text/x-wiki Scaling of WALP test case on Intel Q9550. Hippo rev35. b6ca048a5258caed8ef19f0b0a93e70c602eac72 189 188 2008-12-07T15:53:52Z Oliver 2 uploaded a new version of "[[Image:Scaling Q9550.png]]" wikitext text/x-wiki Scaling of WALP test case on Intel Q9550. Hippo rev35. b6ca048a5258caed8ef19f0b0a93e70c602eac72 6 57 185 2008-12-07T15:35:56Z Oliver 2 walp test rev 35 on dual quad core xeon E5420 2.5 GHz wikitext text/x-wiki walp test rev 35 on dual quad core xeon E5420 2.5 GHz 497ac0ef960d8136b24ed0786c2ea5817db65aab 6 58 196 2008-12-07T21:12:29Z Oliver 2 Scaling of Hippo rev 35 walp test on AMD Phenom X4 9840 wikitext text/x-wiki Scaling of Hippo rev 35 walp test on AMD Phenom X4 9840 881dd16189d9836cfb58248bdc008c15433b6232 12 7 201 135 2008-12-08T10:30:30Z Oliver 2 CSS wikitext text/x-wiki This page should tell you how to work with this Wiki &ndash; it's not complicated, promise! (In fact, the whole point of a wiki is to make it as easy for the user as possible to document whatever there is worth documenting). ==Editing an existing page== # Select the ''Edit'' link at the top. # Type or simply copy and paste text, eg from your editor, shell, or an email, and use the ''preview'' button. # Once it looks sort-of right commit your changes by clicking ''save page''. The Media Wiki page has a comprehensive list of the [http://meta.wikipedia.org/wiki/MediaWiki_User%27s_Guide:_Editing_overview#The_wiki_markup Wiki markup] but you can also look at the code of existing pages (edit the page but don't save it) or use the formatting buttons at the top of your editing box. The most important thing is just to put something on the page and not to worry too much about formatting. If in doubt simply leave one initial space and everything gets formatted verbatim; anything resembling an URL will be turned into a link (or enclose it in <nowiki>'[' and ']'</nowiki>). ==Editing a new page== If you click on a red link then you enter a non-existing page. This is not bad: Simply start editing it and ''write it yourself''. You can't make mistakes. Just do it. ==Creating a new page== To make a non-existing page you simply insert the link into an existing page, it appears in red, you click it and then edit it. == Signing your name == Sometimes this is useful: three tildes <nowiki>~~~</nowiki> signs your name like this: [[User:Oliver|Oliver]]; four <nowiki>~~~~</nowiki> dates it too: [[User:Oliver|Oliver]] 18:32, 24 January 2006 (EST) == Categories == [http://meta.wikimedia.org/wiki/Help:Category '''Categories''' in MediaWiki] provide automatic indexes that are useful as tables of contents. See the Special Page '''[[Special:Categories]]''' for a list of all defined categories. * You '''define a category''' by adding one or more special tags at the end of a page: add <tt><nowiki>[[</nowiki>Category:''Category name''<nowiki>]]</nowiki></tt> to the page's wikitext source. For instance, add to page that describes analysis scripts for Charmm <nowiki>[[Category:Hippo]]</nowiki> <nowiki>[[Category:Analysis]]</nowiki> : as the last two lines. This will implicitly define the categories [[:Category:Analysis]] and [[:Category:Hippo]]. * The '''category pages''' can also be edited. In addition, the wiki software adds an alphabetically sorted list of all pages in the category. This makes a category useful as an entry point into a subject. ** One ''must'' edit a category page for the wiki to create the indexed list (even if it is just an empty edit). ** It is also possible to add another category to a category page: This will turn this category in a subcategory on the other category page. * In order to '''reference a category within a page as a normal wiki link''' (without adding the page to the category) prefix the link name with a colon. For example: <tt><nowiki>[[:</nowiki>Category:Analysis<nowiki>]]</nowiki></tt>. == Page maintenance == === Redirection === A 'symbolic link' to another pages is created with the [http://meta.wikimedia.org/wiki/Help:Redirection REDIRECT] command: <nowiki>#REDIRECT [[</nowiki>''page''<nowiki>]]</nowiki> ==Highlighting sourcecode== Wikimedia can do syntax highlighting for over a dozen programming languages, including c, python, perl, fortran, and c++. Just surround the code with a tag of the name of the language. For example: <pre> <python> import re lines = file("ifconf.log").readlines() l_iter = iter(lines) nodes = [] for l in l_iter: if l[:7] == "compute": node = l.split('.')[0] temp = l_iter.next().split() iface, addr = temp[0], temp[4] nodes.append([node, iface, addr]) </python> </pre> Gives you <python> import re lines = file("ifconf.log").readlines() l_iter = iter(lines) nodes = [] for l in l_iter: if l[:7] == "compute": node = l.split('.')[0] temp = l_iter.next().split() iface, addr = temp[0], temp[4] nodes.append([node, iface, addr]) </python> ==Inserting Gnuplot graphs== You can insert gnuplot graphs directly into mediawiki by using the <tt>gnuplot</tt> tag. For example: <pre> <gnuplot> set output 'func_approx.png' plot '-' using 1:2 t 'quadratic approximation' with linesp lt 1 lw 3, \ '-' using 1:2 t 'cubic approximation' with linesp lt 2 lw 3 1 2 2 4 3 8 4 16 e 1 3 2 9 3 27 4 81 e </gnuplot> </pre> Gives you the following: <gnuplot> set output 'func_approx.png' plot '-' using 1:2 t 'quadratic approximation' with linesp lt 1 lw 3, \ '-' using 1:2 t 'cubic approximation' with linesp lt 2 lw 3 1 2 2 4 3 8 4 16 e 1 3 2 9 3 27 4 81 e </gnuplot> == Adding bibliographic references (specifically [http://www.pubmed.gov PubMed]) == You can insert bibliographic references into pages by using the <tt><nowiki><cite></nowiki></tt> and <tt><nowiki><biblio></nowiki></tt> tags. This uses the PubMed id number (pmid) found at the bottom of the abstract listing for a particular article. Mediawiki will go to [http://www.pubmed.gov PubMed] and pull the citation information for the reference. Using the key in front of the pmid assignment within the <tt><nowiki><cite></nowiki></tt> tag (see example below) gives you a reference to the article within the current page. For example, although you can obmit the pmid and simply format the reference yourself. <pre> Recent papers from the Woolf lab <cite>jcp2005 proteins2005 jcp2004</cite>: ===Bibliography=== <biblio> #jcp2005 pmid=15847458 #proteins2005 pmid=15828005 #jcp2004 pmid=15634036 </biblio> </pre> Will give you this: Recent papers from the Woolf lab <cite>jcp2005 proteins2005 jcp2004</cite>: <b>Bibliography</b> <biblio> #jcp2005 pmid=15847458 #proteins2005 pmid=15828005 #jcp2004 pmid=15634036 </biblio> == Images == The following shows two methods of how to incorporate an image in a wiki page. === Upload === The image is uploaded to the webserver and resides in the wiki (somewhere... you don't need to know where, it's a secret) # first [[Special:Upload|upload]] it (use the link in the toolbox on the left) # enter a wiki link such as <tt><nowiki>[[Image:Gbim.jpg|200px]] </nowiki></tt> into the text. [[Image:Gbim.jpg|200px]] [[Image:Gbim.jpg|thumb|right|150px|Insertion of a peptide into a Generalized Born implicit membrane.]] An exhaustive description of the image capabilities are discussed in the [http://en.wikipedia.org/wiki/Wikipedia:Extended_image_syntax Wikipedia Extended Image Syntax]. Most importantly, if you want to change the size of the image, add a size option <tt>|''size''px</tt> option (<tt>|200px</tt> in the example above). The new version of MediaWiki gives you a plethora of options to add captions, float the image to left or right, change sizes, show it as a (fast) thumbnail, ... <tt><nowiki>[[Image:Gbim.jpg|thumb|right|150px|Insertion of a peptide into a Generalized Born implicit membrane.]]</nowiki></tt> gives a thumbnail image floating on the right hand side. == Styles == One can directly edit the [http://www.w3.org/Style/CSS/ Cascading Style Sheets] (CSS). The most important one is [[Mediawiki:Common.css]] – be careful, all changes directly affect every user. See the [http://www.mediawiki.org/wiki/Manual:Interface/Stylesheets Mediawiki Stylesheet Manual] for details and there is also the useful [http://www.mediawiki.org/wiki/Manual:FAQ Mediawiki FAQ] on customizing the Interface. == Links == If you want to gain an in-depth knowledge of working with this Wiki then have a look at these links: === Wikipedia edit help documents === * Wikipedia's [http://en.wikipedia.org/wiki/Wikipedia:How_to_edit_a_page full listing of wiki editing commands] (make sure you come back here to edit... otherwise you will be editing Wikipedia) * Wikipedia [http://en.wikipedia.org/wiki/Wikipedia:Extended_image_syntax Extended Image Syntax] for all your image inclusion needs * Syntax of [http://en.wikipedia.org/wiki/Help:Table Table] commands === MediaWiki documents === The [http://wiki.biowerkzeug.org/ Biowerkzeug Wiki] uses the [http://www.mediawiki.org/wiki MediaWiki] software. For more on MediaWiki see the following links: * [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] * [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list] * [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ] * [http://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list] [[Category:Help]] 4a3b345a86c2ee4d5c667f61b8847be22fa7d155 208 201 2008-12-08T11:02:30Z Oliver 2 /* Styles */ wikitext text/x-wiki This page should tell you how to work with this Wiki &ndash; it's not complicated, promise! (In fact, the whole point of a wiki is to make it as easy for the user as possible to document whatever there is worth documenting). ==Editing an existing page== # Select the ''Edit'' link at the top. # Type or simply copy and paste text, eg from your editor, shell, or an email, and use the ''preview'' button. # Once it looks sort-of right commit your changes by clicking ''save page''. The Media Wiki page has a comprehensive list of the [http://meta.wikipedia.org/wiki/MediaWiki_User%27s_Guide:_Editing_overview#The_wiki_markup Wiki markup] but you can also look at the code of existing pages (edit the page but don't save it) or use the formatting buttons at the top of your editing box. The most important thing is just to put something on the page and not to worry too much about formatting. If in doubt simply leave one initial space and everything gets formatted verbatim; anything resembling an URL will be turned into a link (or enclose it in <nowiki>'[' and ']'</nowiki>). ==Editing a new page== If you click on a red link then you enter a non-existing page. This is not bad: Simply start editing it and ''write it yourself''. You can't make mistakes. Just do it. ==Creating a new page== To make a non-existing page you simply insert the link into an existing page, it appears in red, you click it and then edit it. == Signing your name == Sometimes this is useful: three tildes <nowiki>~~~</nowiki> signs your name like this: [[User:Oliver|Oliver]]; four <nowiki>~~~~</nowiki> dates it too: [[User:Oliver|Oliver]] 18:32, 24 January 2006 (EST) == Categories == [http://meta.wikimedia.org/wiki/Help:Category '''Categories''' in MediaWiki] provide automatic indexes that are useful as tables of contents. See the Special Page '''[[Special:Categories]]''' for a list of all defined categories. * You '''define a category''' by adding one or more special tags at the end of a page: add <tt><nowiki>[[</nowiki>Category:''Category name''<nowiki>]]</nowiki></tt> to the page's wikitext source. For instance, add to page that describes analysis scripts for Charmm <nowiki>[[Category:Hippo]]</nowiki> <nowiki>[[Category:Analysis]]</nowiki> : as the last two lines. This will implicitly define the categories [[:Category:Analysis]] and [[:Category:Hippo]]. * The '''category pages''' can also be edited. In addition, the wiki software adds an alphabetically sorted list of all pages in the category. This makes a category useful as an entry point into a subject. ** One ''must'' edit a category page for the wiki to create the indexed list (even if it is just an empty edit). ** It is also possible to add another category to a category page: This will turn this category in a subcategory on the other category page. * In order to '''reference a category within a page as a normal wiki link''' (without adding the page to the category) prefix the link name with a colon. For example: <tt><nowiki>[[:</nowiki>Category:Analysis<nowiki>]]</nowiki></tt>. == Page maintenance == === Redirection === A 'symbolic link' to another pages is created with the [http://meta.wikimedia.org/wiki/Help:Redirection REDIRECT] command: <nowiki>#REDIRECT [[</nowiki>''page''<nowiki>]]</nowiki> ==Highlighting sourcecode== Wikimedia can do syntax highlighting for over a dozen programming languages, including c, python, perl, fortran, and c++. Just surround the code with a tag of the name of the language. For example: <pre> <python> import re lines = file("ifconf.log").readlines() l_iter = iter(lines) nodes = [] for l in l_iter: if l[:7] == "compute": node = l.split('.')[0] temp = l_iter.next().split() iface, addr = temp[0], temp[4] nodes.append([node, iface, addr]) </python> </pre> Gives you <python> import re lines = file("ifconf.log").readlines() l_iter = iter(lines) nodes = [] for l in l_iter: if l[:7] == "compute": node = l.split('.')[0] temp = l_iter.next().split() iface, addr = temp[0], temp[4] nodes.append([node, iface, addr]) </python> ==Inserting Gnuplot graphs== You can insert gnuplot graphs directly into mediawiki by using the <tt>gnuplot</tt> tag. For example: <pre> <gnuplot> set output 'func_approx.png' plot '-' using 1:2 t 'quadratic approximation' with linesp lt 1 lw 3, \ '-' using 1:2 t 'cubic approximation' with linesp lt 2 lw 3 1 2 2 4 3 8 4 16 e 1 3 2 9 3 27 4 81 e </gnuplot> </pre> Gives you the following: <gnuplot> set output 'func_approx.png' plot '-' using 1:2 t 'quadratic approximation' with linesp lt 1 lw 3, \ '-' using 1:2 t 'cubic approximation' with linesp lt 2 lw 3 1 2 2 4 3 8 4 16 e 1 3 2 9 3 27 4 81 e </gnuplot> == Adding bibliographic references (specifically [http://www.pubmed.gov PubMed]) == You can insert bibliographic references into pages by using the <tt><nowiki><cite></nowiki></tt> and <tt><nowiki><biblio></nowiki></tt> tags. This uses the PubMed id number (pmid) found at the bottom of the abstract listing for a particular article. Mediawiki will go to [http://www.pubmed.gov PubMed] and pull the citation information for the reference. Using the key in front of the pmid assignment within the <tt><nowiki><cite></nowiki></tt> tag (see example below) gives you a reference to the article within the current page. For example, although you can obmit the pmid and simply format the reference yourself. <pre> Recent papers from the Woolf lab <cite>jcp2005 proteins2005 jcp2004</cite>: ===Bibliography=== <biblio> #jcp2005 pmid=15847458 #proteins2005 pmid=15828005 #jcp2004 pmid=15634036 </biblio> </pre> Will give you this: Recent papers from the Woolf lab <cite>jcp2005 proteins2005 jcp2004</cite>: <b>Bibliography</b> <biblio> #jcp2005 pmid=15847458 #proteins2005 pmid=15828005 #jcp2004 pmid=15634036 </biblio> == Images == The following shows two methods of how to incorporate an image in a wiki page. === Upload === The image is uploaded to the webserver and resides in the wiki (somewhere... you don't need to know where, it's a secret) # first [[Special:Upload|upload]] it (use the link in the toolbox on the left) # enter a wiki link such as <tt><nowiki>[[Image:Gbim.jpg|200px]] </nowiki></tt> into the text. [[Image:Gbim.jpg|200px]] [[Image:Gbim.jpg|thumb|right|150px|Insertion of a peptide into a Generalized Born implicit membrane.]] An exhaustive description of the image capabilities are discussed in the [http://en.wikipedia.org/wiki/Wikipedia:Extended_image_syntax Wikipedia Extended Image Syntax]. Most importantly, if you want to change the size of the image, add a size option <tt>|''size''px</tt> option (<tt>|200px</tt> in the example above). The new version of MediaWiki gives you a plethora of options to add captions, float the image to left or right, change sizes, show it as a (fast) thumbnail, ... <tt><nowiki>[[Image:Gbim.jpg|thumb|right|150px|Insertion of a peptide into a Generalized Born implicit membrane.]]</nowiki></tt> gives a thumbnail image floating on the right hand side. == Styles == One can directly edit the [http://www.w3.org/Style/CSS/ Cascading Style Sheets] (CSS). The most important one is [[Mediawiki:Common.css]] – be careful, all changes directly affect every user. See the [http://www.mediawiki.org/wiki/Manual:Interface/Stylesheets Mediawiki Stylesheet Manual] for details and there is also the useful [http://www.mediawiki.org/wiki/Manual:FAQ Mediawiki FAQ] on customizing the Interface. [http://en.wikipedia.org/wiki/Help:User_style Wikipedia's Help:User_style] has a lot of howto information. == Links == If you want to gain an in-depth knowledge of working with this Wiki then have a look at these links: === Wikipedia edit help documents === * Wikipedia's [http://en.wikipedia.org/wiki/Wikipedia:How_to_edit_a_page full listing of wiki editing commands] (make sure you come back here to edit... otherwise you will be editing Wikipedia) * Wikipedia [http://en.wikipedia.org/wiki/Wikipedia:Extended_image_syntax Extended Image Syntax] for all your image inclusion needs * Syntax of [http://en.wikipedia.org/wiki/Help:Table Table] commands === MediaWiki documents === The [http://wiki.biowerkzeug.org/ Biowerkzeug Wiki] uses the [http://www.mediawiki.org/wiki MediaWiki] software. For more on MediaWiki see the following links: * [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] * [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list] * [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ] * [http://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list] [[Category:Help]] c0867a97cc5f7704c0bf05ed0a5f36becfa04484 212 208 2008-12-08T15:45:30Z Kaihsu 10 /* Highlighting sourcecode */ wikitext text/x-wiki This page should tell you how to work with this Wiki &ndash; it's not complicated, promise! (In fact, the whole point of a wiki is to make it as easy for the user as possible to document whatever there is worth documenting). ==Editing an existing page== # Select the ''Edit'' link at the top. # Type or simply copy and paste text, eg from your editor, shell, or an email, and use the ''preview'' button. # Once it looks sort-of right commit your changes by clicking ''save page''. The Media Wiki page has a comprehensive list of the [http://meta.wikipedia.org/wiki/MediaWiki_User%27s_Guide:_Editing_overview#The_wiki_markup Wiki markup] but you can also look at the code of existing pages (edit the page but don't save it) or use the formatting buttons at the top of your editing box. The most important thing is just to put something on the page and not to worry too much about formatting. If in doubt simply leave one initial space and everything gets formatted verbatim; anything resembling an URL will be turned into a link (or enclose it in <nowiki>'[' and ']'</nowiki>). ==Editing a new page== If you click on a red link then you enter a non-existing page. This is not bad: Simply start editing it and ''write it yourself''. You can't make mistakes. Just do it. ==Creating a new page== To make a non-existing page you simply insert the link into an existing page, it appears in red, you click it and then edit it. == Signing your name == Sometimes this is useful: three tildes <nowiki>~~~</nowiki> signs your name like this: [[User:Oliver|Oliver]]; four <nowiki>~~~~</nowiki> dates it too: [[User:Oliver|Oliver]] 18:32, 24 January 2006 (EST) == Categories == [http://meta.wikimedia.org/wiki/Help:Category '''Categories''' in MediaWiki] provide automatic indexes that are useful as tables of contents. See the Special Page '''[[Special:Categories]]''' for a list of all defined categories. * You '''define a category''' by adding one or more special tags at the end of a page: add <tt><nowiki>[[</nowiki>Category:''Category name''<nowiki>]]</nowiki></tt> to the page's wikitext source. For instance, add to page that describes analysis scripts for Charmm <nowiki>[[Category:Hippo]]</nowiki> <nowiki>[[Category:Analysis]]</nowiki> : as the last two lines. This will implicitly define the categories [[:Category:Analysis]] and [[:Category:Hippo]]. * The '''category pages''' can also be edited. In addition, the wiki software adds an alphabetically sorted list of all pages in the category. This makes a category useful as an entry point into a subject. ** One ''must'' edit a category page for the wiki to create the indexed list (even if it is just an empty edit). ** It is also possible to add another category to a category page: This will turn this category in a subcategory on the other category page. * In order to '''reference a category within a page as a normal wiki link''' (without adding the page to the category) prefix the link name with a colon. For example: <tt><nowiki>[[:</nowiki>Category:Analysis<nowiki>]]</nowiki></tt>. == Page maintenance == === Redirection === A 'symbolic link' to another pages is created with the [http://meta.wikimedia.org/wiki/Help:Redirection REDIRECT] command: <nowiki>#REDIRECT [[</nowiki>''page''<nowiki>]]</nowiki> ==Highlighting sourcecode== Wikimedia can do syntax highlighting for over a dozen programming languages, including c, python, perl, fortran, and c++. Just surround the code with a tag of the name of the language. For example: <pre> <source lang="python"> import re lines = file("ifconf.log").readlines() l_iter = iter(lines) nodes = [] for l in l_iter: if l[:7] == "compute": node = l.split('.')[0] temp = l_iter.next().split() iface, addr = temp[0], temp[4] nodes.append([node, iface, addr]) </source> </pre> Gives you <source lang="python"> import re lines = file("ifconf.log").readlines() l_iter = iter(lines) nodes = [] for l in l_iter: if l[:7] == "compute": node = l.split('.')[0] temp = l_iter.next().split() iface, addr = temp[0], temp[4] nodes.append([node, iface, addr]) </source> ==Inserting Gnuplot graphs== You can insert gnuplot graphs directly into mediawiki by using the <tt>gnuplot</tt> tag. For example: <pre> <gnuplot> set output 'func_approx.png' plot '-' using 1:2 t 'quadratic approximation' with linesp lt 1 lw 3, \ '-' using 1:2 t 'cubic approximation' with linesp lt 2 lw 3 1 2 2 4 3 8 4 16 e 1 3 2 9 3 27 4 81 e </gnuplot> </pre> Gives you the following: <gnuplot> set output 'func_approx.png' plot '-' using 1:2 t 'quadratic approximation' with linesp lt 1 lw 3, \ '-' using 1:2 t 'cubic approximation' with linesp lt 2 lw 3 1 2 2 4 3 8 4 16 e 1 3 2 9 3 27 4 81 e </gnuplot> == Adding bibliographic references (specifically [http://www.pubmed.gov PubMed]) == You can insert bibliographic references into pages by using the <tt><nowiki><cite></nowiki></tt> and <tt><nowiki><biblio></nowiki></tt> tags. This uses the PubMed id number (pmid) found at the bottom of the abstract listing for a particular article. Mediawiki will go to [http://www.pubmed.gov PubMed] and pull the citation information for the reference. Using the key in front of the pmid assignment within the <tt><nowiki><cite></nowiki></tt> tag (see example below) gives you a reference to the article within the current page. For example, although you can obmit the pmid and simply format the reference yourself. <pre> Recent papers from the Woolf lab <cite>jcp2005 proteins2005 jcp2004</cite>: ===Bibliography=== <biblio> #jcp2005 pmid=15847458 #proteins2005 pmid=15828005 #jcp2004 pmid=15634036 </biblio> </pre> Will give you this: Recent papers from the Woolf lab <cite>jcp2005 proteins2005 jcp2004</cite>: <b>Bibliography</b> <biblio> #jcp2005 pmid=15847458 #proteins2005 pmid=15828005 #jcp2004 pmid=15634036 </biblio> == Images == The following shows two methods of how to incorporate an image in a wiki page. === Upload === The image is uploaded to the webserver and resides in the wiki (somewhere... you don't need to know where, it's a secret) # first [[Special:Upload|upload]] it (use the link in the toolbox on the left) # enter a wiki link such as <tt><nowiki>[[Image:Gbim.jpg|200px]] </nowiki></tt> into the text. [[Image:Gbim.jpg|200px]] [[Image:Gbim.jpg|thumb|right|150px|Insertion of a peptide into a Generalized Born implicit membrane.]] An exhaustive description of the image capabilities are discussed in the [http://en.wikipedia.org/wiki/Wikipedia:Extended_image_syntax Wikipedia Extended Image Syntax]. Most importantly, if you want to change the size of the image, add a size option <tt>|''size''px</tt> option (<tt>|200px</tt> in the example above). The new version of MediaWiki gives you a plethora of options to add captions, float the image to left or right, change sizes, show it as a (fast) thumbnail, ... <tt><nowiki>[[Image:Gbim.jpg|thumb|right|150px|Insertion of a peptide into a Generalized Born implicit membrane.]]</nowiki></tt> gives a thumbnail image floating on the right hand side. == Styles == One can directly edit the [http://www.w3.org/Style/CSS/ Cascading Style Sheets] (CSS). The most important one is [[Mediawiki:Common.css]] – be careful, all changes directly affect every user. See the [http://www.mediawiki.org/wiki/Manual:Interface/Stylesheets Mediawiki Stylesheet Manual] for details and there is also the useful [http://www.mediawiki.org/wiki/Manual:FAQ Mediawiki FAQ] on customizing the Interface. [http://en.wikipedia.org/wiki/Help:User_style Wikipedia's Help:User_style] has a lot of howto information. == Links == If you want to gain an in-depth knowledge of working with this Wiki then have a look at these links: === Wikipedia edit help documents === * Wikipedia's [http://en.wikipedia.org/wiki/Wikipedia:How_to_edit_a_page full listing of wiki editing commands] (make sure you come back here to edit... otherwise you will be editing Wikipedia) * Wikipedia [http://en.wikipedia.org/wiki/Wikipedia:Extended_image_syntax Extended Image Syntax] for all your image inclusion needs * Syntax of [http://en.wikipedia.org/wiki/Help:Table Table] commands === MediaWiki documents === The [http://wiki.biowerkzeug.org/ Biowerkzeug Wiki] uses the [http://www.mediawiki.org/wiki MediaWiki] software. For more on MediaWiki see the following links: * [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] * [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list] * [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ] * [http://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list] [[Category:Help]] 58f6e886ba2fafbb2825312e093a4cfab2b085dd 213 212 2008-12-08T15:46:37Z Kaihsu 10 /* Highlighting sourcecode */ wikitext text/x-wiki This page should tell you how to work with this Wiki &ndash; it's not complicated, promise! (In fact, the whole point of a wiki is to make it as easy for the user as possible to document whatever there is worth documenting). ==Editing an existing page== # Select the ''Edit'' link at the top. # Type or simply copy and paste text, eg from your editor, shell, or an email, and use the ''preview'' button. # Once it looks sort-of right commit your changes by clicking ''save page''. The Media Wiki page has a comprehensive list of the [http://meta.wikipedia.org/wiki/MediaWiki_User%27s_Guide:_Editing_overview#The_wiki_markup Wiki markup] but you can also look at the code of existing pages (edit the page but don't save it) or use the formatting buttons at the top of your editing box. The most important thing is just to put something on the page and not to worry too much about formatting. If in doubt simply leave one initial space and everything gets formatted verbatim; anything resembling an URL will be turned into a link (or enclose it in <nowiki>'[' and ']'</nowiki>). ==Editing a new page== If you click on a red link then you enter a non-existing page. This is not bad: Simply start editing it and ''write it yourself''. You can't make mistakes. Just do it. ==Creating a new page== To make a non-existing page you simply insert the link into an existing page, it appears in red, you click it and then edit it. == Signing your name == Sometimes this is useful: three tildes <nowiki>~~~</nowiki> signs your name like this: [[User:Oliver|Oliver]]; four <nowiki>~~~~</nowiki> dates it too: [[User:Oliver|Oliver]] 18:32, 24 January 2006 (EST) == Categories == [http://meta.wikimedia.org/wiki/Help:Category '''Categories''' in MediaWiki] provide automatic indexes that are useful as tables of contents. See the Special Page '''[[Special:Categories]]''' for a list of all defined categories. * You '''define a category''' by adding one or more special tags at the end of a page: add <tt><nowiki>[[</nowiki>Category:''Category name''<nowiki>]]</nowiki></tt> to the page's wikitext source. For instance, add to page that describes analysis scripts for Charmm <nowiki>[[Category:Hippo]]</nowiki> <nowiki>[[Category:Analysis]]</nowiki> : as the last two lines. This will implicitly define the categories [[:Category:Analysis]] and [[:Category:Hippo]]. * The '''category pages''' can also be edited. In addition, the wiki software adds an alphabetically sorted list of all pages in the category. This makes a category useful as an entry point into a subject. ** One ''must'' edit a category page for the wiki to create the indexed list (even if it is just an empty edit). ** It is also possible to add another category to a category page: This will turn this category in a subcategory on the other category page. * In order to '''reference a category within a page as a normal wiki link''' (without adding the page to the category) prefix the link name with a colon. For example: <tt><nowiki>[[:</nowiki>Category:Analysis<nowiki>]]</nowiki></tt>. == Page maintenance == === Redirection === A 'symbolic link' to another pages is created with the [http://meta.wikimedia.org/wiki/Help:Redirection REDIRECT] command: <nowiki>#REDIRECT [[</nowiki>''page''<nowiki>]]</nowiki> ==Highlighting sourcecode== MediaWiki can do syntax highlighting for over a dozen programming languages, including C, Python, Perl, Fortran, and C++. Just surround the code with a <tt>source</tt> tag of the name of the language in the variable <tt>lang</tt>. For example: <pre> <source lang="python"> import re lines = file("ifconf.log").readlines() l_iter = iter(lines) nodes = [] for l in l_iter: if l[:7] == "compute": node = l.split('.')[0] temp = l_iter.next().split() iface, addr = temp[0], temp[4] nodes.append([node, iface, addr]) </source> </pre> Gives you <source lang="python"> import re lines = file("ifconf.log").readlines() l_iter = iter(lines) nodes = [] for l in l_iter: if l[:7] == "compute": node = l.split('.')[0] temp = l_iter.next().split() iface, addr = temp[0], temp[4] nodes.append([node, iface, addr]) </source> ==Inserting Gnuplot graphs== You can insert gnuplot graphs directly into mediawiki by using the <tt>gnuplot</tt> tag. For example: <pre> <gnuplot> set output 'func_approx.png' plot '-' using 1:2 t 'quadratic approximation' with linesp lt 1 lw 3, \ '-' using 1:2 t 'cubic approximation' with linesp lt 2 lw 3 1 2 2 4 3 8 4 16 e 1 3 2 9 3 27 4 81 e </gnuplot> </pre> Gives you the following: <gnuplot> set output 'func_approx.png' plot '-' using 1:2 t 'quadratic approximation' with linesp lt 1 lw 3, \ '-' using 1:2 t 'cubic approximation' with linesp lt 2 lw 3 1 2 2 4 3 8 4 16 e 1 3 2 9 3 27 4 81 e </gnuplot> == Adding bibliographic references (specifically [http://www.pubmed.gov PubMed]) == You can insert bibliographic references into pages by using the <tt><nowiki><cite></nowiki></tt> and <tt><nowiki><biblio></nowiki></tt> tags. This uses the PubMed id number (pmid) found at the bottom of the abstract listing for a particular article. Mediawiki will go to [http://www.pubmed.gov PubMed] and pull the citation information for the reference. Using the key in front of the pmid assignment within the <tt><nowiki><cite></nowiki></tt> tag (see example below) gives you a reference to the article within the current page. For example, although you can obmit the pmid and simply format the reference yourself. <pre> Recent papers from the Woolf lab <cite>jcp2005 proteins2005 jcp2004</cite>: ===Bibliography=== <biblio> #jcp2005 pmid=15847458 #proteins2005 pmid=15828005 #jcp2004 pmid=15634036 </biblio> </pre> Will give you this: Recent papers from the Woolf lab <cite>jcp2005 proteins2005 jcp2004</cite>: <b>Bibliography</b> <biblio> #jcp2005 pmid=15847458 #proteins2005 pmid=15828005 #jcp2004 pmid=15634036 </biblio> == Images == The following shows two methods of how to incorporate an image in a wiki page. === Upload === The image is uploaded to the webserver and resides in the wiki (somewhere... you don't need to know where, it's a secret) # first [[Special:Upload|upload]] it (use the link in the toolbox on the left) # enter a wiki link such as <tt><nowiki>[[Image:Gbim.jpg|200px]] </nowiki></tt> into the text. [[Image:Gbim.jpg|200px]] [[Image:Gbim.jpg|thumb|right|150px|Insertion of a peptide into a Generalized Born implicit membrane.]] An exhaustive description of the image capabilities are discussed in the [http://en.wikipedia.org/wiki/Wikipedia:Extended_image_syntax Wikipedia Extended Image Syntax]. Most importantly, if you want to change the size of the image, add a size option <tt>|''size''px</tt> option (<tt>|200px</tt> in the example above). The new version of MediaWiki gives you a plethora of options to add captions, float the image to left or right, change sizes, show it as a (fast) thumbnail, ... <tt><nowiki>[[Image:Gbim.jpg|thumb|right|150px|Insertion of a peptide into a Generalized Born implicit membrane.]]</nowiki></tt> gives a thumbnail image floating on the right hand side. == Styles == One can directly edit the [http://www.w3.org/Style/CSS/ Cascading Style Sheets] (CSS). The most important one is [[Mediawiki:Common.css]] – be careful, all changes directly affect every user. See the [http://www.mediawiki.org/wiki/Manual:Interface/Stylesheets Mediawiki Stylesheet Manual] for details and there is also the useful [http://www.mediawiki.org/wiki/Manual:FAQ Mediawiki FAQ] on customizing the Interface. [http://en.wikipedia.org/wiki/Help:User_style Wikipedia's Help:User_style] has a lot of howto information. == Links == If you want to gain an in-depth knowledge of working with this Wiki then have a look at these links: === Wikipedia edit help documents === * Wikipedia's [http://en.wikipedia.org/wiki/Wikipedia:How_to_edit_a_page full listing of wiki editing commands] (make sure you come back here to edit... otherwise you will be editing Wikipedia) * Wikipedia [http://en.wikipedia.org/wiki/Wikipedia:Extended_image_syntax Extended Image Syntax] for all your image inclusion needs * Syntax of [http://en.wikipedia.org/wiki/Help:Table Table] commands === MediaWiki documents === The [http://wiki.biowerkzeug.org/ Biowerkzeug Wiki] uses the [http://www.mediawiki.org/wiki MediaWiki] software. For more on MediaWiki see the following links: * [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] * [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list] * [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ] * [http://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list] [[Category:Help]] 954d8be4de4381403040e8877d9ecae1a8cc5af2 8 8 202 117 2008-12-08T10:35:12Z Oliver 2 table caption css text/css /* CSS placed here will be applied to all skins */ /* Copied from http://de.wikipedia.org/wiki/MediaWiki:Common.css : "+++++ 3. NEUE [[Hauptseite|HAUPTSEITE]] (ab 2006) +++++" */ /* Kategorie verbergen */ body.page-Hauptseite #catlinks { display:none; } #hauptseite h2 { background-color: #d8e8ff; border: 1px solid #8898bf; font-size: 1em; font-weight: bold; margin-top: 0; margin-bottom: 0; padding-top: 0.1em; padding-bottom: 0.1em; } #hauptseite .inhalt { background-color: #ffffff; border: 1px solid #8898bf; border-top: 0px solid white; padding: 0.3em 0.8em 0.4em 0.8em; } #hauptseite .inhalt hr { background-color: #8898bf; color: #8898bf; height: 1px; margin:0.5em 0; padding: 0; } #hauptseite .inhalt .mehr { clear: both; font-size: 95%; margin-top: 0.8em; text-align: right; } .hauptseite-oben, .hauptseite-links, .hauptseite-rechts { margin-bottom: 1em; } .hauptseite-links { margin-right: 0.5em; } .hauptseite-rechts { margin-left: 0.5em; } .hauptseite-oben h2, .hauptseite-unten h2 { text-align: center; } .hauptseite-oben .inhalt .portale { font-weight: bold; margin-top: 0.2em; margin-bottom: 0.2em; } .hauptseite-oben .inhalt .intern { font-size: 90%; text-align: center; } .hauptseite-links h2, .hauptseite-rechts h2 { text-indent: 0.8em; } #hauptseite-schwesterprojekte .inhalt a { font-weight: bold; } /* p.catlinks span a[href*="/wiki/Kategorie:Arbeitskategorie"] { display:none } wegen HIDDENCAT nicht mehr notwendig */ /* Remove underline from IPA links */ .IPA a:link, .IPA a:visited { text-decoration: none; } span.Unicode { font-family: 'Code2000', 'Sun-ExtA', 'Arial Unicode MS', 'NSimSun', sans-serif; } span.Unicode1 { font-family: 'Code2001', 'Quivira', 'MPH 2B Damase', sans-serif; } span.Unicode2 { font-family: 'Sun-ExtB', 'Code2002', sans-serif; } span.IPA { font-family: 'Quivira', 'Code2000', 'Sun-ExtA', 'DejaVu Sans', 'Gentium', 'Arial Unicode MS', 'Lucida Sans Unicode', sans-serif; } span.IAST { font-family: 'Code2000', 'SunExtA', 'Arial Unicode MS', sans-serif; } span.altitalisch { font-family: 'Quivira', 'Code2001', 'MPH 2B Damase', sans-serif; } span.gotisch { font-family: 'Quivira', 'Code2001', 'MPH 2B Damase', sans-serif; } span.hebrew { font-family: 'Quivira', 'Sun-ExtA', 'Arial Unicode MS', 'SBL Hebrew', 'Code2000', 'MPH 2B Damase', sans-serif; } span.spanAr { font-family: 'Arial Unicode MS', 'Code2000', 'MPH 2B Damase', 'DejaVu Sans', sans-serif; } span.music-symbol { font-family: 'Musical Symbols', 'Euterpe', 'Code2001', sans-serif; } /* Standardmäßige Ausblendung der Flagged-Revisions-Backlog-Sitenotice */ #mw-oldreviewed-notice { display: none; } /* copied from http://meta.wikimedia.org/wiki/MediaWiki:Common.css */ /***** ** Table formatting *****/ table.wikitable, table.prettytable { margin:1em 1em 1em 0; background:#F9F9F9; border:1px #AAA solid; border-collapse:collapse; } table.wikitable th, table.wikitable td, table.prettytable th, table.prettytable td { border:1px #AAA solid; padding:0.2em; } table.wikitable th, table.prettytable th { background:#F2F2F2; text-align:center; } table.wikitable caption, table.prettytable caption { margin-left:inherit; margin-right:inherit; border:1px #AAA solid; background: #F0F0F0; } /***** ** box formatting *****/ .infobox { float:right; clear:right; margin-bottom:0.5em; margin-left:1em; padding:0.2em; border:1px solid #AAA; background:#F9F9F9; color:black; } .infobox td, .infobox th { vertical-align:top; } .infobox caption { font-size:larger; margin-left:inherit; } .infobox.bordered { border-collapse:collapse; } .infobox.bordered td, .infobox.bordered th { border:1px solid #AAA; } .infobox.bordered .borderless td, .infobox.bordered .borderless th { border:0; } /* Change the external link icon to an Adobe icon for all PDF files */ /* (in browsers that support these CSS selectors, like Mozilla and Opera) */ #bodyContent a[href$=".pdf"].external, #bodyContent a[href*=".pdf?"].external, #bodyContent a[href*=".pdf#"].external, #bodyContent a[href$=".PDF"].external, #bodyContent a[href*=".PDF?"].external, #bodyContent a[href*=".PDF#"].external { background: url(http://upload.wikimedia.org/wikipedia/commons/thumb/2/23/Icons-mini-file_acrobat.gif/15px-Icons-mini-file_acrobat.gif) center right no-repeat; padding-right: 16px; } /* Change the external link icon to an Adobe icon anywhere the PDFlink class */ /* is used (notably Template:PDFlink). This works in IE, unlike the above. */ span.PDFlink a { background: url(http://upload.wikimedia.org/wikipedia/commons/thumb/2/23/Icons-mini-file_acrobat.gif/15px-Icons-mini-file_acrobat.gif) center right no-repeat !important; padding-right: 17px !important; } 7c4a2e0927900785e162e456ce2281ba8d2c916d 203 202 2008-12-08T10:37:17Z Oliver 2 table left aligned txt css text/css /* CSS placed here will be applied to all skins */ /* Copied from http://de.wikipedia.org/wiki/MediaWiki:Common.css : "+++++ 3. NEUE [[Hauptseite|HAUPTSEITE]] (ab 2006) +++++" */ /* Kategorie verbergen */ body.page-Hauptseite #catlinks { display:none; } #hauptseite h2 { background-color: #d8e8ff; border: 1px solid #8898bf; font-size: 1em; font-weight: bold; margin-top: 0; margin-bottom: 0; padding-top: 0.1em; padding-bottom: 0.1em; } #hauptseite .inhalt { background-color: #ffffff; border: 1px solid #8898bf; border-top: 0px solid white; padding: 0.3em 0.8em 0.4em 0.8em; } #hauptseite .inhalt hr { background-color: #8898bf; color: #8898bf; height: 1px; margin:0.5em 0; padding: 0; } #hauptseite .inhalt .mehr { clear: both; font-size: 95%; margin-top: 0.8em; text-align: right; } .hauptseite-oben, .hauptseite-links, .hauptseite-rechts { margin-bottom: 1em; } .hauptseite-links { margin-right: 0.5em; } .hauptseite-rechts { margin-left: 0.5em; } .hauptseite-oben h2, .hauptseite-unten h2 { text-align: center; } .hauptseite-oben .inhalt .portale { font-weight: bold; margin-top: 0.2em; margin-bottom: 0.2em; } .hauptseite-oben .inhalt .intern { font-size: 90%; text-align: center; } .hauptseite-links h2, .hauptseite-rechts h2 { text-indent: 0.8em; } #hauptseite-schwesterprojekte .inhalt a { font-weight: bold; } /* p.catlinks span a[href*="/wiki/Kategorie:Arbeitskategorie"] { display:none } wegen HIDDENCAT nicht mehr notwendig */ /* Remove underline from IPA links */ .IPA a:link, .IPA a:visited { text-decoration: none; } span.Unicode { font-family: 'Code2000', 'Sun-ExtA', 'Arial Unicode MS', 'NSimSun', sans-serif; } span.Unicode1 { font-family: 'Code2001', 'Quivira', 'MPH 2B Damase', sans-serif; } span.Unicode2 { font-family: 'Sun-ExtB', 'Code2002', sans-serif; } span.IPA { font-family: 'Quivira', 'Code2000', 'Sun-ExtA', 'DejaVu Sans', 'Gentium', 'Arial Unicode MS', 'Lucida Sans Unicode', sans-serif; } span.IAST { font-family: 'Code2000', 'SunExtA', 'Arial Unicode MS', sans-serif; } span.altitalisch { font-family: 'Quivira', 'Code2001', 'MPH 2B Damase', sans-serif; } span.gotisch { font-family: 'Quivira', 'Code2001', 'MPH 2B Damase', sans-serif; } span.hebrew { font-family: 'Quivira', 'Sun-ExtA', 'Arial Unicode MS', 'SBL Hebrew', 'Code2000', 'MPH 2B Damase', sans-serif; } span.spanAr { font-family: 'Arial Unicode MS', 'Code2000', 'MPH 2B Damase', 'DejaVu Sans', sans-serif; } span.music-symbol { font-family: 'Musical Symbols', 'Euterpe', 'Code2001', sans-serif; } /* Standardmäßige Ausblendung der Flagged-Revisions-Backlog-Sitenotice */ #mw-oldreviewed-notice { display: none; } /* copied from http://meta.wikimedia.org/wiki/MediaWiki:Common.css */ /***** ** Table formatting *****/ table.wikitable, table.prettytable { margin:1em 1em 1em 0; background:#F9F9F9; border:1px #AAA solid; border-collapse:collapse; } table.wikitable th, table.wikitable td, table.prettytable th, table.prettytable td { border:1px #AAA solid; padding:0.2em; } table.wikitable th, table.prettytable th { background:#F2F2F2; text-align:center; } table.wikitable caption, table.prettytable caption { margin-left:inherit; margin-right:inherit; border:1px #AAA solid; background: #E0E0E0; text-align: left; } /***** ** box formatting *****/ .infobox { float:right; clear:right; margin-bottom:0.5em; margin-left:1em; padding:0.2em; border:1px solid #AAA; background:#F9F9F9; color:black; } .infobox td, .infobox th { vertical-align:top; } .infobox caption { font-size:larger; margin-left:inherit; } .infobox.bordered { border-collapse:collapse; } .infobox.bordered td, .infobox.bordered th { border:1px solid #AAA; } .infobox.bordered .borderless td, .infobox.bordered .borderless th { border:0; } /* Change the external link icon to an Adobe icon for all PDF files */ /* (in browsers that support these CSS selectors, like Mozilla and Opera) */ #bodyContent a[href$=".pdf"].external, #bodyContent a[href*=".pdf?"].external, #bodyContent a[href*=".pdf#"].external, #bodyContent a[href$=".PDF"].external, #bodyContent a[href*=".PDF?"].external, #bodyContent a[href*=".PDF#"].external { background: url(http://upload.wikimedia.org/wikipedia/commons/thumb/2/23/Icons-mini-file_acrobat.gif/15px-Icons-mini-file_acrobat.gif) center right no-repeat; padding-right: 16px; } /* Change the external link icon to an Adobe icon anywhere the PDFlink class */ /* is used (notably Template:PDFlink). This works in IE, unlike the above. */ span.PDFlink a { background: url(http://upload.wikimedia.org/wikipedia/commons/thumb/2/23/Icons-mini-file_acrobat.gif/15px-Icons-mini-file_acrobat.gif) center right no-repeat !important; padding-right: 17px !important; } b8122da65ee517e6e717454816b4f5d62d56c723 0 50 204 200 2008-12-08T10:53:27Z Oliver 2 scaling in main table wikitext text/x-wiki == Single processor performance == As a basic performance test we run the simulations in the <tt>test</tt> directory with these commands (on Linux): cd testjobs time ./calc_testjobs <ul> <li>We report the ''user'' time.</li> <li>CPU properties are found with <pre>cat /proc/cpuinfo</pre> and model names from [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors List of Intelmicroprocessors] for Intel (also see the [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors#Detailed_x86_architecture_microprocessor_lists detailed lists of Intel x86 CPUs]) and [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors List of AMD microprocessors] for AMD cpus (also see the [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors#Detailed_microprocessor_release_lists detailed lists of AMD CPUs]).</li> <li>Also report the binary used (<tt>hippo</tt> or <tt>hippo_p3</tt>) and the revision.</li> <li>Note that these tests only utilize a ''single core''.</li> <li>These results only give a rough idea of the ''relative'' performance of different architectures.</li> </ul> Please add your own results. {| class="wikitable sortable" |+ Benchmark (single core) and [[#Scaling|scaling]] results on multiple cores/cpus. ! vendor ! model ! GHz ! cores ! time/min ! binary ! revision ! scaling |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Core_2_microprocessors#.22Yorkfield.22_.2845_nm.29 Core 2 Quad Q9550] | 2.83 | 4 | 1:04 | hippo | rev32 <!-- deathspud --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Core_2_microprocessors#.22Yorkfield.22_.2845_nm.29 Core 2 Quad Q9550] | 2.83 | 4 | 1:05 | hippo | rev35 <!-- deathspud --> | [[Image:Scaling Q9550.png|thumb|none|Intel Quad Core Q9550 2.8 GHz]] |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Core_2_microprocessors#.22Yorkfield.22_.2845_nm.29 Core 2 Quad Q9550] | 2.83 | 4 | 1:06 | hippo_p3 | rev32 <!-- deathspud --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28standard-voltage.2C_45_nm.29 Quad Core Xeon E5420] | 2.5 | 4 | 1:16 | hippo | rev35 <!-- darthtater --> | [[Image:Scaling E5420.png|thumb|none|Dual Intel Quad Core Xeon E5420 2.5 GHz]] |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28standard-voltage.2C_45_nm.29 Quad Core Xeon E5420] | 2.5 | 4 | 1:16 | hippo | rev32 <!-- darthtater --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410] | 2.33 | 4 | 1:27 | hippo | rev32 |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410] | 2.33 | 4 | 1:31 | hippo_p3 | rev32 <!-- tinman --> |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Phenom_microprocessors#.22Agena.22_.28B2_.26_B3.2C_65_nm.29 Phenom X4 9850] | 2.5 | 4 | 1:36 | hippo_p3 | rev32 <!-- greenwulf --> |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Phenom_microprocessors#.22Agena.22_.28B2_.26_B3.2C_65_nm.29 Phenom X4 9850] | 2.5 | 4 | 1:37 | hippo_p3 | rev35 <!-- greenwulf --> | [[Image:Scaling AMD X4 9840.png|thumb|none|AMD Phenom X4 9850 Quad Core 2.5 GHz]] |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Opteron_microprocessors#Opteron_200-series_.22SledgeHammer.22_.28B3_.26_C0_.26_CG.2C_130_nm.29 Opteron 248] | 2.2 | 1 | 2:18 | hippo_p3 | rev32 <!-- gltph --> |- | Intel | Core Duo T2300 (Mac Mini) | 1.66 | 2 | 2:41 | hippo_p3 | rev32 <!-- abbondanza --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Prestonia.22_.28standard-voltage.2C_130_nm.29 Xeon 2.4] | 2.4 | 1 | 3:03 | hippo_p3 | rev26 <!-- timberwulf --> |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Athlon_XP_microprocessors#Athlon_XP_.22Palomino.22_.28Model_6.2C_180_nm.29 Athlon XP 1800+] | 1.53 | 1 | 4:30 | hippo_p3 | rev26 |} <small>(You don't ''have'' to link to the CPU wikipedia page; just put down whatever you got and even if you're unsure. If in doubt just put the output from cat /proc/cpuinfo | \ awk 'BEGIN {FS=":"}; \ /vendor_id/ {vendor=$2}; \ /model name/ {model=$2}; \ /cpu MHz/ {GHz=$2/1000}; \ /siblings/ {cores=$2}; \ END {printf("|-\n| %s\n| %s\n| %.1f\n| %d\n| TIME\n| ?\n| ?\n", vendor, model, GHz, cores)}' into the wiki table and replace ''TIME'' by what you measured.</small> == Scaling == All tests were run with Hippo beta rev35 on empty systems. See remarks on the [[Talk:Performance#Scaling|test methodology]]. In the table below, '''# cpus''' really means how many independent cores are available. {| class="wikitable sortable" |+ Scaling of the Hippo WALP test case using OpenMP on single-board machines ! vendor ! # cpus ! walltime and scaling |- | Intel | 4 | [[Image:Scaling Q9550.png|thumb|none|Intel Quad Core Q9550 2.8 GHz]] |- | Intel | 8 | [[Image:Scaling E5420.png|thumb|none|Dual Intel Quad Core Xeon E5420 2.5 GHz]] |- | AMD | 4 | [[Image:Scaling AMD X4 9840.png|thumb|none|AMD Phenom X4 9850 Quad Core 2.5 GHz]] |} 633da49d123f0e9779f1fd2912cb2e1c7e5aea87 205 204 2008-12-08T10:54:38Z Oliver 2 /* Single processor performance */ wikitext text/x-wiki == Single processor performance == As a basic performance test we run the simulations in the <tt>test</tt> directory with these commands (on Linux): cd testjobs time ./calc_testjobs <ul> <li>We report the ''user'' time.</li> <li>CPU properties are found with <pre>cat /proc/cpuinfo</pre> and model names from [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors List of Intelmicroprocessors] for Intel (also see the [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors#Detailed_x86_architecture_microprocessor_lists detailed lists of Intel x86 CPUs]) and [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors List of AMD microprocessors] for AMD cpus (also see the [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors#Detailed_microprocessor_release_lists detailed lists of AMD CPUs]).</li> <li>Also report the binary used (<tt>hippo</tt> or <tt>hippo_p3</tt>) and the revision.</li> <li>Note that these tests only utilize a ''single core''.</li> <li>These results only give a rough idea of the ''relative'' performance of different architectures.</li> <li>The timings have errorbars of about ±2s</li> </ul> Please add your own results. {| class="wikitable sortable" |+ Benchmark (single core) and [[#Scaling|scaling]] results on multiple cores/cpus. ! vendor ! model ! GHz ! cores ! time/min ! binary ! revision ! scaling |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Core_2_microprocessors#.22Yorkfield.22_.2845_nm.29 Core 2 Quad Q9550] | 2.83 | 4 | 1:04 | hippo | rev32 <!-- deathspud --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Core_2_microprocessors#.22Yorkfield.22_.2845_nm.29 Core 2 Quad Q9550] | 2.83 | 4 | 1:05 | hippo | rev35 <!-- deathspud --> | [[Image:Scaling Q9550.png|thumb|none|Intel Quad Core Q9550 2.8 GHz]] |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Core_2_microprocessors#.22Yorkfield.22_.2845_nm.29 Core 2 Quad Q9550] | 2.83 | 4 | 1:06 | hippo_p3 | rev32 <!-- deathspud --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28standard-voltage.2C_45_nm.29 Quad Core Xeon E5420] | 2.5 | 4 | 1:16 | hippo | rev35 <!-- darthtater --> | [[Image:Scaling E5420.png|thumb|none|Dual Intel Quad Core Xeon E5420 2.5 GHz]] |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28standard-voltage.2C_45_nm.29 Quad Core Xeon E5420] | 2.5 | 4 | 1:16 | hippo | rev32 <!-- darthtater --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410] | 2.33 | 4 | 1:27 | hippo | rev32 |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410] | 2.33 | 4 | 1:31 | hippo_p3 | rev32 <!-- tinman --> |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Phenom_microprocessors#.22Agena.22_.28B2_.26_B3.2C_65_nm.29 Phenom X4 9850] | 2.5 | 4 | 1:36 | hippo_p3 | rev32 <!-- greenwulf --> |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Phenom_microprocessors#.22Agena.22_.28B2_.26_B3.2C_65_nm.29 Phenom X4 9850] | 2.5 | 4 | 1:37 | hippo_p3 | rev35 <!-- greenwulf --> | [[Image:Scaling AMD X4 9840.png|thumb|none|AMD Phenom X4 9850 Quad Core 2.5 GHz]] |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Opteron_microprocessors#Opteron_200-series_.22SledgeHammer.22_.28B3_.26_C0_.26_CG.2C_130_nm.29 Opteron 248] | 2.2 | 1 | 2:18 | hippo_p3 | rev32 <!-- gltph --> |- | Intel | Core Duo T2300 (Mac Mini) | 1.66 | 2 | 2:41 | hippo_p3 | rev32 <!-- abbondanza --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Prestonia.22_.28standard-voltage.2C_130_nm.29 Xeon 2.4] | 2.4 | 1 | 3:03 | hippo_p3 | rev26 <!-- timberwulf --> |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Athlon_XP_microprocessors#Athlon_XP_.22Palomino.22_.28Model_6.2C_180_nm.29 Athlon XP 1800+] | 1.53 | 1 | 4:30 | hippo_p3 | rev26 |} <small>(You don't ''have'' to link to the CPU wikipedia page; just put down whatever you got and even if you're unsure. If in doubt just put the output from cat /proc/cpuinfo | \ awk 'BEGIN {FS=":"}; \ /vendor_id/ {vendor=$2}; \ /model name/ {model=$2}; \ /cpu MHz/ {GHz=$2/1000}; \ /siblings/ {cores=$2}; \ END {printf("|-\n| %s\n| %s\n| %.1f\n| %d\n| TIME\n| ?\n| ?\n", vendor, model, GHz, cores)}' into the wiki table and replace ''TIME'' by what you measured.</small> == Scaling == All tests were run with Hippo beta rev35 on empty systems. See remarks on the [[Talk:Performance#Scaling|test methodology]]. In the table below, '''# cpus''' really means how many independent cores are available. {| class="wikitable sortable" |+ Scaling of the Hippo WALP test case using OpenMP on single-board machines ! vendor ! # cpus ! walltime and scaling |- | Intel | 4 | [[Image:Scaling Q9550.png|thumb|none|Intel Quad Core Q9550 2.8 GHz]] |- | Intel | 8 | [[Image:Scaling E5420.png|thumb|none|Dual Intel Quad Core Xeon E5420 2.5 GHz]] |- | AMD | 4 | [[Image:Scaling AMD X4 9840.png|thumb|none|AMD Phenom X4 9850 Quad Core 2.5 GHz]] |} 522e3e25840f9d4fe4f1d660b5f6115617b66fdc 206 205 2008-12-08T10:56:35Z Oliver 2 /* Single processor performance */ wikitext text/x-wiki == Single processor performance == As a basic performance test we run the simulations in the <tt>test</tt> directory with these commands (on Linux): cd testjobs time ./calc_testjobs <ul> <li>We report the ''user'' time.</li> <li>CPU properties are found with <pre>cat /proc/cpuinfo</pre> and model names from [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors List of Intelmicroprocessors] for Intel (also see the [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors#Detailed_x86_architecture_microprocessor_lists detailed lists of Intel x86 CPUs]) and [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors List of AMD microprocessors] for AMD cpus (also see the [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors#Detailed_microprocessor_release_lists detailed lists of AMD CPUs]).</li> <li>Also report the binary used (<tt>hippo</tt> or <tt>hippo_p3</tt>) and the revision.</li> <li>Note that these tests only utilize a ''single core''.</li> <li>These results only give a rough idea of the ''relative'' performance of different architectures.</li> <li>The timings have errorbars of about ±2s</li> </ul> Please add your own results. {| class="wikitable sortable" |+ Benchmark (single core) and [[#Scaling|scaling]] results on multiple cores/cpus. ! vendor ! model ! GHz ! cores ! time/min ! binary ! revision ! scaling |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Core_2_microprocessors#.22Yorkfield.22_.2845_nm.29 Core 2 Quad Q9550] | 2.83 | 4 | 1:04 | hippo | rev32 <!-- deathspud --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Core_2_microprocessors#.22Yorkfield.22_.2845_nm.29 Core 2 Quad Q9550] | 2.83 | 4 | 1:05 | hippo | rev35 <!-- deathspud --> | [[Image:Scaling Q9550.png|thumb|none|Intel Quad Core Q9550 2.8 GHz]] |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Core_2_microprocessors#.22Yorkfield.22_.2845_nm.29 Core 2 Quad Q9550] | 2.83 | 4 | 1:06 | hippo_p3 | rev32 <!-- deathspud --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28standard-voltage.2C_45_nm.29 Quad Core Xeon E5420] | 2.5 | 8 = 2x4 | 1:16 | hippo | rev35 <!-- darthtater --> | [[Image:Scaling E5420.png|thumb|none|Dual Intel Quad Core Xeon E5420 2.5 GHz]] |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28standard-voltage.2C_45_nm.29 Quad Core Xeon E5420] | 2.5 | 4 | 1:16 | hippo | rev32 <!-- darthtater --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410] | 2.33 | 4 | 1:27 | hippo | rev32 |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410] | 2.33 | 4 | 1:31 | hippo_p3 | rev32 <!-- tinman --> |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Phenom_microprocessors#.22Agena.22_.28B2_.26_B3.2C_65_nm.29 Phenom X4 9850] | 2.5 | 4 | 1:36 | hippo_p3 | rev32 <!-- greenwulf --> |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Phenom_microprocessors#.22Agena.22_.28B2_.26_B3.2C_65_nm.29 Phenom X4 9850] | 2.5 | 4 | 1:37 | hippo_p3 | rev35 <!-- greenwulf --> | [[Image:Scaling AMD X4 9840.png|thumb|none|AMD Phenom X4 9850 Quad Core 2.5 GHz]] |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Opteron_microprocessors#Opteron_200-series_.22SledgeHammer.22_.28B3_.26_C0_.26_CG.2C_130_nm.29 Opteron 248] | 2.2 | 1 | 2:18 | hippo_p3 | rev32 <!-- gltph --> |- | Intel | Core Duo T2300 (Mac Mini) | 1.66 | 2 | 2:41 | hippo_p3 | rev32 <!-- abbondanza --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Prestonia.22_.28standard-voltage.2C_130_nm.29 Xeon 2.4] | 2.4 | 1 | 3:03 | hippo_p3 | rev26 <!-- timberwulf --> |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Athlon_XP_microprocessors#Athlon_XP_.22Palomino.22_.28Model_6.2C_180_nm.29 Athlon XP 1800+] | 1.53 | 1 | 4:30 | hippo_p3 | rev26 |} <small>(You don't ''have'' to link to the CPU wikipedia page; just put down whatever you got and even if you're unsure. If in doubt just put the output from cat /proc/cpuinfo | \ awk 'BEGIN {FS=":"}; \ /vendor_id/ {vendor=$2}; \ /model name/ {model=$2}; \ /cpu MHz/ {GHz=$2/1000}; \ /siblings/ {cores=$2}; \ END {printf("|-\n| %s\n| %s\n| %.1f\n| %d\n| TIME\n| ?\n| ?\n", vendor, model, GHz, cores)}' into the wiki table and replace ''TIME'' by what you measured.</small> == Scaling == All tests were run with Hippo beta rev35 on empty systems. See remarks on the [[Talk:Performance#Scaling|test methodology]]. In the table below, '''# cpus''' really means how many independent cores are available. {| class="wikitable sortable" |+ Scaling of the Hippo WALP test case using OpenMP on single-board machines ! vendor ! # cpus ! walltime and scaling |- | Intel | 4 | [[Image:Scaling Q9550.png|thumb|none|Intel Quad Core Q9550 2.8 GHz]] |- | Intel | 8 | [[Image:Scaling E5420.png|thumb|none|Dual Intel Quad Core Xeon E5420 2.5 GHz]] |- | AMD | 4 | [[Image:Scaling AMD X4 9840.png|thumb|none|AMD Phenom X4 9850 Quad Core 2.5 GHz]] |} 32ab92ac92803cbe9651008eac41aebc12f4d912 207 206 2008-12-08T11:00:46Z Oliver 2 /* Single processor performance */ wikitext text/x-wiki == Single processor performance == As a basic performance test we run the simulations in the <tt>test</tt> directory with these commands (on Linux): cd testjobs time ./calc_testjobs <ul> <li>We report the ''user'' time.</li> <li>CPU properties are found with <pre>cat /proc/cpuinfo</pre> and model names from [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors List of Intelmicroprocessors] for Intel (also see the [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors#Detailed_x86_architecture_microprocessor_lists detailed lists of Intel x86 CPUs]) and [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors List of AMD microprocessors] for AMD cpus (also see the [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors#Detailed_microprocessor_release_lists detailed lists of AMD CPUs]).</li> <li>Also report the binary used (<tt>hippo</tt> or <tt>hippo_p3</tt>) and the revision.</li> <li>Note that these tests only utilize a ''single core''.</li> <li>These results only give a rough idea of the ''relative'' performance of different architectures.</li> <li>The timings have errorbars of about ±2s</li> </ul> Please add your own results. {| class="wikitable sortable" |+ Benchmark (single core) and [[#Scaling|scaling]] results on multiple cores/cpus. '''cores''' indicates how many cores are available to the user on this cpu ''or'' the maximum number of cores on the node that were used for benchmarking scaling. ! vendor ! model ! GHz ! cores ! time/min ! binary ! revision ! scaling |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Core_2_microprocessors#.22Yorkfield.22_.2845_nm.29 Core 2 Quad Q9550] | 2.83 | 4 | 1:04 | hippo | rev32 <!-- deathspud --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Core_2_microprocessors#.22Yorkfield.22_.2845_nm.29 Core 2 Quad Q9550] | 2.83 | 4 | 1:05 | hippo | rev35 <!-- deathspud --> | [[Image:Scaling Q9550.png|thumb|none|Intel Quad Core Q9550 2.8 GHz]] |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Core_2_microprocessors#.22Yorkfield.22_.2845_nm.29 Core 2 Quad Q9550] | 2.83 | 4 | 1:06 | hippo_p3 | rev32 <!-- deathspud --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28standard-voltage.2C_45_nm.29 Quad Core Xeon E5420] | 2.5 | 8 = 2x4 | 1:16 | hippo | rev35 <!-- darthtater --> | [[Image:Scaling E5420.png|thumb|none|Dual Intel Quad Core Xeon E5420 2.5 GHz]] |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28standard-voltage.2C_45_nm.29 Quad Core Xeon E5420] | 2.5 | 4 | 1:16 | hippo | rev32 <!-- darthtater --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410] | 2.33 | 4 | 1:27 | hippo | rev32 |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410] | 2.33 | 4 | 1:31 | hippo_p3 | rev32 <!-- tinman --> |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Phenom_microprocessors#.22Agena.22_.28B2_.26_B3.2C_65_nm.29 Phenom X4 9850] | 2.5 | 4 | 1:36 | hippo_p3 | rev32 <!-- greenwulf --> |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Phenom_microprocessors#.22Agena.22_.28B2_.26_B3.2C_65_nm.29 Phenom X4 9850] | 2.5 | 4 | 1:37 | hippo_p3 | rev35 <!-- greenwulf --> | [[Image:Scaling AMD X4 9840.png|thumb|none|AMD Phenom X4 9850 Quad Core 2.5 GHz]] |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Opteron_microprocessors#Opteron_200-series_.22SledgeHammer.22_.28B3_.26_C0_.26_CG.2C_130_nm.29 Opteron 248] | 2.2 | 1 | 2:18 | hippo_p3 | rev32 <!-- gltph --> |- | Intel | Core Duo T2300 (Mac Mini) | 1.66 | 2 | 2:41 | hippo_p3 | rev32 <!-- abbondanza --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Prestonia.22_.28standard-voltage.2C_130_nm.29 Xeon 2.4] | 2.4 | 1 | 3:03 | hippo_p3 | rev26 <!-- timberwulf --> |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Athlon_XP_microprocessors#Athlon_XP_.22Palomino.22_.28Model_6.2C_180_nm.29 Athlon XP 1800+] | 1.53 | 1 | 4:30 | hippo_p3 | rev26 |} <small>(You don't ''have'' to link to the CPU wikipedia page; just put down whatever you got and even if you're unsure. If in doubt just put the output from cat /proc/cpuinfo | \ awk 'BEGIN {FS=":"}; \ /vendor_id/ {vendor=$2}; \ /model name/ {model=$2}; \ /cpu MHz/ {GHz=$2/1000}; \ /siblings/ {cores=$2}; \ END {printf("|-\n| %s\n| %s\n| %.1f\n| %d\n| TIME\n| ?\n| ?\n", vendor, model, GHz, cores)}' into the wiki table and replace ''TIME'' by what you measured.</small> == Scaling == All tests were run with Hippo beta rev35 on empty systems. See remarks on the [[Talk:Performance#Scaling|test methodology]]. In the table below, '''# cpus''' really means how many independent cores are available. {| class="wikitable sortable" |+ Scaling of the Hippo WALP test case using OpenMP on single-board machines ! vendor ! # cpus ! walltime and scaling |- | Intel | 4 | [[Image:Scaling Q9550.png|thumb|none|Intel Quad Core Q9550 2.8 GHz]] |- | Intel | 8 | [[Image:Scaling E5420.png|thumb|none|Dual Intel Quad Core Xeon E5420 2.5 GHz]] |- | AMD | 4 | [[Image:Scaling AMD X4 9840.png|thumb|none|AMD Phenom X4 9850 Quad Core 2.5 GHz]] |} fc7bec231d1b6c3efb0c134f29559ca9175feb5f 214 207 2008-12-08T15:49:51Z Kaihsu 10 use <source/> wikitext text/x-wiki == Single processor performance == As a basic performance test we run the simulations in the <tt>test</tt> directory with these commands (on Linux): cd testjobs time ./calc_testjobs <ul> <li>We report the ''user'' time.</li> <li>CPU properties are found with <pre>cat /proc/cpuinfo</pre> and model names from [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors List of Intelmicroprocessors] for Intel (also see the [http://en.wikipedia.org/wiki/List_of_Intel_microprocessors#Detailed_x86_architecture_microprocessor_lists detailed lists of Intel x86 CPUs]) and [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors List of AMD microprocessors] for AMD cpus (also see the [http://en.wikipedia.org/wiki/List_of_AMD_microprocessors#Detailed_microprocessor_release_lists detailed lists of AMD CPUs]).</li> <li>Also report the binary used (<tt>hippo</tt> or <tt>hippo_p3</tt>) and the revision.</li> <li>Note that these tests only utilize a ''single core''.</li> <li>These results only give a rough idea of the ''relative'' performance of different architectures.</li> <li>The timings have errorbars of about ±2s</li> </ul> Please add your own results. {| class="wikitable sortable" |+ Benchmark (single core) and [[#Scaling|scaling]] results on multiple cores/cpus. '''cores''' indicates how many cores are available to the user on this cpu ''or'' the maximum number of cores on the node that were used for benchmarking scaling. ! vendor ! model ! GHz ! cores ! time/min ! binary ! revision ! scaling |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Core_2_microprocessors#.22Yorkfield.22_.2845_nm.29 Core 2 Quad Q9550] | 2.83 | 4 | 1:04 | hippo | rev32 <!-- deathspud --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Core_2_microprocessors#.22Yorkfield.22_.2845_nm.29 Core 2 Quad Q9550] | 2.83 | 4 | 1:05 | hippo | rev35 <!-- deathspud --> | [[Image:Scaling Q9550.png|thumb|none|Intel Quad Core Q9550 2.8 GHz]] |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Core_2_microprocessors#.22Yorkfield.22_.2845_nm.29 Core 2 Quad Q9550] | 2.83 | 4 | 1:06 | hippo_p3 | rev32 <!-- deathspud --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28standard-voltage.2C_45_nm.29 Quad Core Xeon E5420] | 2.5 | 8 = 2x4 | 1:16 | hippo | rev35 <!-- darthtater --> | [[Image:Scaling E5420.png|thumb|none|Dual Intel Quad Core Xeon E5420 2.5 GHz]] |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28standard-voltage.2C_45_nm.29 Quad Core Xeon E5420] | 2.5 | 4 | 1:16 | hippo | rev32 <!-- darthtater --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410] | 2.33 | 4 | 1:27 | hippo | rev32 |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Harpertown.22_.28low-voltage.2C_45_nm.29 Quad Core Xeon L5410] | 2.33 | 4 | 1:31 | hippo_p3 | rev32 <!-- tinman --> |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Phenom_microprocessors#.22Agena.22_.28B2_.26_B3.2C_65_nm.29 Phenom X4 9850] | 2.5 | 4 | 1:36 | hippo_p3 | rev32 <!-- greenwulf --> |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Phenom_microprocessors#.22Agena.22_.28B2_.26_B3.2C_65_nm.29 Phenom X4 9850] | 2.5 | 4 | 1:37 | hippo_p3 | rev35 <!-- greenwulf --> | [[Image:Scaling AMD X4 9840.png|thumb|none|AMD Phenom X4 9850 Quad Core 2.5 GHz]] |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Opteron_microprocessors#Opteron_200-series_.22SledgeHammer.22_.28B3_.26_C0_.26_CG.2C_130_nm.29 Opteron 248] | 2.2 | 1 | 2:18 | hippo_p3 | rev32 <!-- gltph --> |- | Intel | Core Duo T2300 (Mac Mini) | 1.66 | 2 | 2:41 | hippo_p3 | rev32 <!-- abbondanza --> |- | Intel | [http://en.wikipedia.org/wiki/List_of_Intel_Xeon_microprocessors#.22Prestonia.22_.28standard-voltage.2C_130_nm.29 Xeon 2.4] | 2.4 | 1 | 3:03 | hippo_p3 | rev26 <!-- timberwulf --> |- | AMD | [http://en.wikipedia.org/wiki/List_of_AMD_Athlon_XP_microprocessors#Athlon_XP_.22Palomino.22_.28Model_6.2C_180_nm.29 Athlon XP 1800+] | 1.53 | 1 | 4:30 | hippo_p3 | rev26 |} <small>(You don't ''have'' to link to the CPU wikipedia page; just put down whatever you got and even if you're unsure. If in doubt just put the output from <source lang="bash"> cat /proc/cpuinfo | \ awk 'BEGIN {FS=":"}; \ /vendor_id/ {vendor=$2}; \ /model name/ {model=$2}; \ /cpu MHz/ {GHz=$2/1000}; \ /siblings/ {cores=$2}; \ END {printf("|-\n| %s\n| %s\n| %.1f\n| %d\n| TIME\n| ?\n| ?\n", vendor, model, GHz, cores)}' </source> into the wiki table and replace ''TIME'' by what you measured.</small> == Scaling == All tests were run with Hippo beta rev35 on empty systems. See remarks on the [[Talk:Performance#Scaling|test methodology]]. In the table below, '''# cpus''' really means how many independent cores are available. {| class="wikitable sortable" |+ Scaling of the Hippo WALP test case using OpenMP on single-board machines ! vendor ! # cpus ! walltime and scaling |- | Intel | 4 | [[Image:Scaling Q9550.png|thumb|none|Intel Quad Core Q9550 2.8 GHz]] |- | Intel | 8 | [[Image:Scaling E5420.png|thumb|none|Dual Intel Quad Core Xeon E5420 2.5 GHz]] |- | AMD | 4 | [[Image:Scaling AMD X4 9840.png|thumb|none|AMD Phenom X4 9850 Quad Core 2.5 GHz]] |} b7e6250a44707949e2ddb9b5d107adaec36edb10 0 54 209 195 2008-12-08T15:41:52Z Kaihsu 10 try <source/> wikitext text/x-wiki This script allows running Hippo benchmarks without having to think too much about finding the correct binary and supplemental files. In addition it gives the total wall time required to run each test case; this can be used for crude benchmarks. * The testing of the mpi binaries is not tested and probably does not work. However, they are ''only'' needed for replica exchange simulations and there are no test cases for those anyway. * [http://forums.biowerkzeug.org/viewtopic.php?f=22&t=6&p=15&hilit=OpenMP#p15 Not all tests support multi-threaded runs] (with OpenMP); these tests ignore the NSLOTS argument. <source lang="bash">#!/bin/bash # $Id: calc_testjobs_linux.sh 2535 2008-12-07 16:07:19Z www-data $ # Running Hippo tests (Linux) # Copyright (c) 2008 Biowerkzeug # Oliver Beckstein <orbeckst@gmail.com> #set -x prog=$(basename $0) CURDIR=${PWD} # defaults (: can be set in environment) : ${HIPPO_DIR:="${CURDIR}/.."} HIPPO_TESTS="hexane_NVT_dp_MD octane_NPT_sp_MC pentadecane_NPT_sp_MD tip3p_NPT_sp_MD trpzip2_GBSA_MC vpu_GBIM_MC walp_octane_NPT_sp_MD" RUN_TESTS=${HIPPO_TESTS} USE_MPI=0 usage="usage $prog [opts] [tests] Run Hippo tests. By default it runs all of them: ${HIPPO_TESTS} OPTIONS: -h help -n number of threads (not possible for all tests) -D directory where we look for Hippo executables [${HIPPO_DIR}] -M use mpi (replica exchange) binaries [${USE_MPI}] Environment variables: HIPPO_DIR overrides -D [${HIPPO_DIR}] " function die () { local msg="$1" err=${2:-1} echo 1>&2 "ERROR: failed in $PWD: ${msg}" cd ${CURDIR} exit $err } NSLOTS=1 # opt processing while getopts hn:D:M: opt; do case $opt in h) echo "$usage"; exit 0;; n) NSLOTS=${OPTARG};; D) HIPPO_DIR=${OPTARG};; M) USE_MPI=${OPTARG};; *) die "Unknown option" 1;; esac done #echo "OPTIND=$OPTIND OPTARG=$OPTARG argv=$*" shift $((OPTIND - 1)) if [ -n "$*" ]; then RUN_TESTS="$*" fi echo "Running the following tests using ${NSLOTS} threads: ${RUN_TESTS}" # find working executable # we'll use the first one that only complain about missing input file # if [ ${USE_MPI} = 0 ]; then echo "Trying standard binaries (with OpenMP)" _HIPPO_BINARIES="hippo hippo_p3" else echo "Testing mpi binaries. Note: these are ONLY needed for replica exchange simulations" _HIPPO_BINARIES="hippo_mpi hippo_p3_mpi" fi HIPPO="not_found" rm -f hippo_input.txt # clean any input files for h in ${_HIPPO_BINARIES}; do exe="${HIPPO_DIR}/${h}" if ${exe} 2>&1 | egrep "^Hippo.*Copyright.*Biowerkzeug" >/dev/null; then HIPPO=${exe} break fi done if [ "${HIPPO}" = "not_found" ]; then ARCH=$(uname -m); OS=$(uname -s); die "No usable hippo executable found; see if there is one at http://www.biowerkzeug.com for your architecture ${ARCH} and operating system ${OS}. " fi echo "Using executable ${HIPPO}" TOPOLOGY=${HIPPO_DIR}/hippo_protein_database.dat FF=${HIPPO_DIR}/oplsaa_forcefield.dat echo "Setting up test directory" rm -rf test mkdir test cd test topdir="${CURDIR}/test" function setup_hippo () { local numthreads=${1:-1} local input=hippo_input.txt cp ${HIPPO} ./hippo || return $? cp ${TOPOLOGY} . || return $? cp ${FF} . || return $? test -e $input || die "Missing run input file $input in $PWD" if [ $NSLOTS -gt 1 ]; then # adjusting for OpenMP run sed -i.orig -e "s/[[:space:]]*openMP numthreads.*/openMP numthreads ${numthreads}/" $input fi return 0 } function run_test () { local testdir="$1" numthreads="${2:-1}" echo "---------------------------------------------------------" cd ${testdir} || die "Cannot 'cd ${testdir}'" setup_hippo ${numthreads} || die "setup_hippo() failed" echo "Set up all files for NSLOTS=${numthreads}" echo "Running hippo test case ${testdir}..." t_start=$(date +%s) ./hippo t_stop=$(date +%s) delta_t=$(( t_stop-t_start )) echo "Completed hippo test case ${testdir} in ${delta_t} seconds, running ${numthreads} threads" echo "BENCHMARK: ${testdir} ${numthreads} ${delta_t}" cd ${topdir} } cp -r ../jobs/* . for t in ${RUN_TESTS}; do run_test $t ${NSLOTS} done echo "Finished running hippo test suite" </source> 146a7579cdcb90e4557fc59a45e78e8a74edb76e 0 55 210 190 2008-12-08T15:43:01Z Kaihsu 10 use <source/> wikitext text/x-wiki Python script that uses [[calc_testjobs_linux.sh]] to benchmark scaling using the ''walp_octane_NPT_sp_MD'' test case. See [[Talk:Performance#Scaling]] for details. <source lang="python"> #!/usr/bin/env python # $Id: test_scaling.py 2534 2008-12-07 15:59:59Z www-data $ # Testing scaling of hippo # Copyright (c) 2008 Biowerkzeug # Oliver Beckstein <orbeckst@gmail.com> from subprocess import Popen,PIPE import sys,re calc_test_jobs = '/home/oliver/Library/Hippo/Benchmark/calc_testjobs_linux.sh' hippo_test_case = 'walp_octane_NPT_sp_MD' filename = "scaling.xvg" figname = "scaling.png" try: maxslots = int(sys.argv[1]) except: print "usage: %s NSLOTS" % sys.argv[0] sys.exit(1) slotrange = (1,maxslots+1) # <--- 1-4 !! benchmark_pattern = re.compile(r'BENCHMARK:\s*(\w+)\s+(?P<NUMTHREADS>[0-9]+)\s+(?P<T_SECONDS>[0-9.]+)') runtime = {} out = open(filename,'w') out.write("# scaling for Hippo\n# numthreads walltime/s scaling\n") for NSLOTS in xrange(*slotrange): print "-- running NSLOTS = %(NSLOTS)d" % vars() p1 = Popen([calc_test_jobs, '-n', str(NSLOTS), hippo_test_case],stdout=PIPE) p2 = Popen(['grep','BENCHMARK:'],stdin=p1.stdout,stdout=PIPE) output = p2.communicate()[0] m = benchmark_pattern.match(output) print "output: ",output, if not m: print "ERROR: no benchmark data found" continue numthreads = int(m.group('NUMTHREADS')) walltime = float(m.group('T_SECONDS')) runtime[numthreads] = walltime scaling = runtime[1]/walltime # runtime[1] is known after the first iteration! out.write("%(numthreads)d %(walltime)f %(scaling)f\n" % vars()) out.close() # Analysis import numpy import pylab N = numpy.sort(runtime.keys()) T = numpy.array([runtime[n] for n in N],dtype=float) S = T[0]/T pylab.clf() pylab.subplot(211) pylab.title('Hippo test case: '+hippo_test_case) pylab.xlabel('cpus') pylab.ylabel('walltime/s') pylab.plot(N,T,'ro-') pylab.subplot(212) pylab.xlabel('cpus') pylab.ylabel('scaling') pylab.plot(N,S,'ro-') pylab.plot([N[0],N[-1]], [1,N[-1]], 'k--') pylab.savefig(figname) print "Saved figure "+figname </source> 68b4af078264e3440f21a99bc7f2a2b23771d756 1 51 211 187 2008-12-08T15:44:06Z Kaihsu 10 /* Scaling */ wikitext text/x-wiki == Integration with tests == We could write a script that does the benchmark while running the test. It would even be possible to automatically post it (with the user's consent, of course). &mdash; [[User:Oliver|Oli]] 16:03, 14 November 2008 (UTC) == Scaling == How to run scaling tests/testing methodology: Use [[test_scaling.py]] which in turn uses [[calc_testjobs_linux.sh]]. cd testjobs test_scaling.py ''NSLOTS'' where ''NSLOTS'' is the maximum number of available cpus/cores. Results are the files scaling.xvg # numbers scaling.png # graphs * Only measures ''wall time'', hence must be run on an empty machine. * Uses <code>date +%s</code> so accuracy is limited to seconds. * No repeat runs; results may vary slightly. Manually: Use updated [[calc_testjobs_linux.sh]] <source lang="bash"> DATA=scaling.xvg MAXSLOTS=8 echo -e "# scaling for Hippo\n# numthreads walltime/s" > $DATA for NSLOTS in `seq $MAXSLOTS`; do echo "-- NSLOTS = $NSLOTS"; ../../calc_testjobs_linux.sh -n $NSLOTS walp_octane_NPT_sp_MD \ | awk '/BENCHMARK/ {print $3, $4}' >> $DATA; done </source> All the above remarks apply here, too. ea5c56d4002587adc7267279ad3aedc8bd90bc47 0 29 215 66 2009-02-07T14:07:06Z Oliver 2 /* MD Analysis libraries */ LOOS wikitext text/x-wiki Running simulations is often the easy bit. The hard bit is to extract meaningful information from the Gigabytes of trajectory data. This list can act as a starting point. For most advanced uses, however, one will probably have to write analysis code in [[python]], [[Perl]], [[tcl]], [[C/C++]], [[bash]] ... or any other language that "gets the job done". == "Native" tools == Many of the [[Molecular dynamics software|MD packages]] come with their own analysis tools or scripting language. Sometimes it is possible to [[convert data formats]] between packages and use the other package's analysis tools. ;[[Gromacs]] analysis tools: oone of the strengths of Gromacs is that it comes with a large number of useful analysis tools that make many of the standard analysis tasks simple to perform ;NAMD/[[VMD]]: VMD can be used through its GUI or by scripting it in [[tcl]] to great effect ;[[Charmm]]: Charmm is feature-rich but its scripting language can cause a steep learning curve ;LAMMPS/[[pizza]]: pizza.py is a python library geared towards output from [[LAMMPS]] ;Amber/[[ptraj]]: command-line based analysis == MD Analysis libraries == ;[[MDAnalysis]]: a python library to analyze dcd trajectories (in conjunction with a psf) ;[http://dirac.cnrs-orleans.fr/MMTK/ MMTK]: Another python-based framework for doing analysis is the ''Molecular Modelling Tool Kit''. However, it does not natively read [[Charmm]] dcd files and hence it can be cumbersome to use. ;[http://membrane.urmc.rochester.edu/Software/LOOS/Docs/main.html LOOS}: The ''Lightweight Object-Oriented Structure library (LOOS)'' from Alan Grossfield's lab provides a lightweight C++ library for analysis of molecular dynamics simulations. This includes parsing a number of PDB variants, as well as the native system description and trajectory formats for CHARMM, NAMD, and Amber. LOOS is not intended to be an all-encompassing library and it is primarily geared towards reading data in and processing rather than manipulating the files and structures and writing them out. == Specialized tools == ;[[HOLE]]: Oliver Smart's program to trace out pore surfaces and estimate single channel conductances. ;CAVER: [http://loschmidt.chemi.muni.cz/caver/index.php CAVER] provides rapid, accurate and fully automated calculation of pathways leading from buried cavities to outside solvent in static and dynamic protein structures. Calculated pathways can be visualized by graphic program PyMol dissecting anatomy and dynamics of entrance tunnels. CAVER allows analysis of any molecular structure including proteins, nucleic acids, inorganic materials, etc. CAVER is available as [http://loschmidt.chemi.muni.cz/caver/online.php online version] or [[PyMol]] plugin suitable for calculation of pathways in discrete protein structures and stand alone version enabling analysis of trajectories from the molecular dynamics simulations. ;[http://swift.cmbi.ru.nl/gv/dssp/ dssp]: ''Definition of secondary structure of proteins given a set of 3D coordinates.'' The DSSP program defines secondary structure, geometrical features and solvent exposure of proteins, given atomic coordinates in Protein Data Bank format. The program does NOT PREDICT protein structure. According to the Science Citation Index (July 1995), the program has been cited in the scientific literature more than 1000 times. ; [http://www.compbio.dundee.ac.uk/manuals/stamp.4.2/stamp.html STAMP]: ''Structural Alignment of Multiple Proteins''. STAMP is a package for the alignment of protein sequence based on three-dimensional (3D) structure. It provides not only multiple alignments and the corresponding `best-fit' superimpositions, but also a systematic and reproducible method for assessing the quality of such alignments. It also provides a method for protein 3D structure data base scanning. In addition to structure comparison, the STAMP package provides input for programs to display and analyse protein sequence alignments and tertiary structures. Please note that, although STAMP outputs a sequence alignment, it is a program for 3D structures, and NOT sequences. ;[[swinker]]: finds and calculates helix hinges. It optionally finds the hinge point and calculates kink and swivel angles. == General purpose mathematical packages == ;[[Scientific Python]] and [[pylab]]: a [[matlab]]-like [[python]] module that has sophisticated analysis and plotting capabilities ;[[matlab]]: ;[[Mathematica]]: ;[[R]]: R is a language and environment for statistical computing and graphics. R provides a wide variety of statistical (linear and nonlinear modelling, classical statistical tests, time-series analysis, classification, clustering, ...) and graphical techniques, and is highly extensible. One of R's strengths is the ease with which well-designed publication-quality plots can be produced, including mathematical symbols and formulae where needed. Great care has been taken over the defaults for the minor design choices in graphics, but the user retains full control. [[Category:Analysis]] [[Category:Software]] bb32a93f23e66fb78d816a4e52af8b4036e0fd48 216 215 2009-02-07T14:07:29Z Oliver 2 /* MD Analysis libraries */ wikitext text/x-wiki Running simulations is often the easy bit. The hard bit is to extract meaningful information from the Gigabytes of trajectory data. This list can act as a starting point. For most advanced uses, however, one will probably have to write analysis code in [[python]], [[Perl]], [[tcl]], [[C/C++]], [[bash]] ... or any other language that "gets the job done". == "Native" tools == Many of the [[Molecular dynamics software|MD packages]] come with their own analysis tools or scripting language. Sometimes it is possible to [[convert data formats]] between packages and use the other package's analysis tools. ;[[Gromacs]] analysis tools: oone of the strengths of Gromacs is that it comes with a large number of useful analysis tools that make many of the standard analysis tasks simple to perform ;NAMD/[[VMD]]: VMD can be used through its GUI or by scripting it in [[tcl]] to great effect ;[[Charmm]]: Charmm is feature-rich but its scripting language can cause a steep learning curve ;LAMMPS/[[pizza]]: pizza.py is a python library geared towards output from [[LAMMPS]] ;Amber/[[ptraj]]: command-line based analysis == MD Analysis libraries == ;[[MDAnalysis]]: a python library to analyze dcd trajectories (in conjunction with a psf) ;[http://dirac.cnrs-orleans.fr/MMTK/ MMTK]: Another python-based framework for doing analysis is the ''Molecular Modelling Tool Kit''. However, it does not natively read [[Charmm]] dcd files and hence it can be cumbersome to use. ;[http://membrane.urmc.rochester.edu/Software/LOOS/Docs/main.html LOOS]: The ''Lightweight Object-Oriented Structure library (LOOS)'' from Alan Grossfield's lab provides a lightweight C++ library for analysis of molecular dynamics simulations. This includes parsing a number of PDB variants, as well as the native system description and trajectory formats for CHARMM, NAMD, and Amber. LOOS is not intended to be an all-encompassing library and it is primarily geared towards reading data in and processing rather than manipulating the files and structures and writing them out. == Specialized tools == ;[[HOLE]]: Oliver Smart's program to trace out pore surfaces and estimate single channel conductances. ;CAVER: [http://loschmidt.chemi.muni.cz/caver/index.php CAVER] provides rapid, accurate and fully automated calculation of pathways leading from buried cavities to outside solvent in static and dynamic protein structures. Calculated pathways can be visualized by graphic program PyMol dissecting anatomy and dynamics of entrance tunnels. CAVER allows analysis of any molecular structure including proteins, nucleic acids, inorganic materials, etc. CAVER is available as [http://loschmidt.chemi.muni.cz/caver/online.php online version] or [[PyMol]] plugin suitable for calculation of pathways in discrete protein structures and stand alone version enabling analysis of trajectories from the molecular dynamics simulations. ;[http://swift.cmbi.ru.nl/gv/dssp/ dssp]: ''Definition of secondary structure of proteins given a set of 3D coordinates.'' The DSSP program defines secondary structure, geometrical features and solvent exposure of proteins, given atomic coordinates in Protein Data Bank format. The program does NOT PREDICT protein structure. According to the Science Citation Index (July 1995), the program has been cited in the scientific literature more than 1000 times. ; [http://www.compbio.dundee.ac.uk/manuals/stamp.4.2/stamp.html STAMP]: ''Structural Alignment of Multiple Proteins''. STAMP is a package for the alignment of protein sequence based on three-dimensional (3D) structure. It provides not only multiple alignments and the corresponding `best-fit' superimpositions, but also a systematic and reproducible method for assessing the quality of such alignments. It also provides a method for protein 3D structure data base scanning. In addition to structure comparison, the STAMP package provides input for programs to display and analyse protein sequence alignments and tertiary structures. Please note that, although STAMP outputs a sequence alignment, it is a program for 3D structures, and NOT sequences. ;[[swinker]]: finds and calculates helix hinges. It optionally finds the hinge point and calculates kink and swivel angles. == General purpose mathematical packages == ;[[Scientific Python]] and [[pylab]]: a [[matlab]]-like [[python]] module that has sophisticated analysis and plotting capabilities ;[[matlab]]: ;[[Mathematica]]: ;[[R]]: R is a language and environment for statistical computing and graphics. R provides a wide variety of statistical (linear and nonlinear modelling, classical statistical tests, time-series analysis, classification, clustering, ...) and graphical techniques, and is highly extensible. One of R's strengths is the ease with which well-designed publication-quality plots can be produced, including mathematical symbols and formulae where needed. Great care has been taken over the defaults for the minor design choices in graphics, but the user retains full control. [[Category:Analysis]] [[Category:Software]] 0818b1cf49cedde269d83002309ce2e20812ba4d 217 216 2009-02-07T14:07:57Z Oliver 2 /* MD Analysis libraries */ wikitext text/x-wiki Running simulations is often the easy bit. The hard bit is to extract meaningful information from the Gigabytes of trajectory data. This list can act as a starting point. For most advanced uses, however, one will probably have to write analysis code in [[python]], [[Perl]], [[tcl]], [[C/C++]], [[bash]] ... or any other language that "gets the job done". == "Native" tools == Many of the [[Molecular dynamics software|MD packages]] come with their own analysis tools or scripting language. Sometimes it is possible to [[convert data formats]] between packages and use the other package's analysis tools. ;[[Gromacs]] analysis tools: oone of the strengths of Gromacs is that it comes with a large number of useful analysis tools that make many of the standard analysis tasks simple to perform ;NAMD/[[VMD]]: VMD can be used through its GUI or by scripting it in [[tcl]] to great effect ;[[Charmm]]: Charmm is feature-rich but its scripting language can cause a steep learning curve ;LAMMPS/[[pizza]]: pizza.py is a python library geared towards output from [[LAMMPS]] ;Amber/[[ptraj]]: command-line based analysis == MD Analysis libraries == ;[http://mdanalysis.googlecode.com/ MDAnalysis]: a python library to analyze dcd trajectories (in conjunction with a psf) ;[http://dirac.cnrs-orleans.fr/MMTK/ MMTK]: Another python-based framework for doing analysis is the ''Molecular Modelling Tool Kit''. However, it does not natively read [[Charmm]] dcd files and hence it can be cumbersome to use. ;[http://membrane.urmc.rochester.edu/Software/LOOS/Docs/main.html LOOS]: The ''Lightweight Object-Oriented Structure library (LOOS)'' from Alan Grossfield's lab provides a lightweight C++ library for analysis of molecular dynamics simulations. This includes parsing a number of PDB variants, as well as the native system description and trajectory formats for CHARMM, NAMD, and Amber. LOOS is not intended to be an all-encompassing library and it is primarily geared towards reading data in and processing rather than manipulating the files and structures and writing them out. == Specialized tools == ;[[HOLE]]: Oliver Smart's program to trace out pore surfaces and estimate single channel conductances. ;CAVER: [http://loschmidt.chemi.muni.cz/caver/index.php CAVER] provides rapid, accurate and fully automated calculation of pathways leading from buried cavities to outside solvent in static and dynamic protein structures. Calculated pathways can be visualized by graphic program PyMol dissecting anatomy and dynamics of entrance tunnels. CAVER allows analysis of any molecular structure including proteins, nucleic acids, inorganic materials, etc. CAVER is available as [http://loschmidt.chemi.muni.cz/caver/online.php online version] or [[PyMol]] plugin suitable for calculation of pathways in discrete protein structures and stand alone version enabling analysis of trajectories from the molecular dynamics simulations. ;[http://swift.cmbi.ru.nl/gv/dssp/ dssp]: ''Definition of secondary structure of proteins given a set of 3D coordinates.'' The DSSP program defines secondary structure, geometrical features and solvent exposure of proteins, given atomic coordinates in Protein Data Bank format. The program does NOT PREDICT protein structure. According to the Science Citation Index (July 1995), the program has been cited in the scientific literature more than 1000 times. ; [http://www.compbio.dundee.ac.uk/manuals/stamp.4.2/stamp.html STAMP]: ''Structural Alignment of Multiple Proteins''. STAMP is a package for the alignment of protein sequence based on three-dimensional (3D) structure. It provides not only multiple alignments and the corresponding `best-fit' superimpositions, but also a systematic and reproducible method for assessing the quality of such alignments. It also provides a method for protein 3D structure data base scanning. In addition to structure comparison, the STAMP package provides input for programs to display and analyse protein sequence alignments and tertiary structures. Please note that, although STAMP outputs a sequence alignment, it is a program for 3D structures, and NOT sequences. ;[[swinker]]: finds and calculates helix hinges. It optionally finds the hinge point and calculates kink and swivel angles. == General purpose mathematical packages == ;[[Scientific Python]] and [[pylab]]: a [[matlab]]-like [[python]] module that has sophisticated analysis and plotting capabilities ;[[matlab]]: ;[[Mathematica]]: ;[[R]]: R is a language and environment for statistical computing and graphics. R provides a wide variety of statistical (linear and nonlinear modelling, classical statistical tests, time-series analysis, classification, clustering, ...) and graphical techniques, and is highly extensible. One of R's strengths is the ease with which well-designed publication-quality plots can be produced, including mathematical symbols and formulae where needed. Great care has been taken over the defaults for the minor design choices in graphics, but the user retains full control. [[Category:Analysis]] [[Category:Software]] 6d76ad4847b9de20ed3d1e8b74693ef75befb25b 218 217 2009-02-07T14:09:24Z Oliver 2 /* Specialized tools */ wikitext text/x-wiki Running simulations is often the easy bit. The hard bit is to extract meaningful information from the Gigabytes of trajectory data. This list can act as a starting point. For most advanced uses, however, one will probably have to write analysis code in [[python]], [[Perl]], [[tcl]], [[C/C++]], [[bash]] ... or any other language that "gets the job done". == "Native" tools == Many of the [[Molecular dynamics software|MD packages]] come with their own analysis tools or scripting language. Sometimes it is possible to [[convert data formats]] between packages and use the other package's analysis tools. ;[[Gromacs]] analysis tools: oone of the strengths of Gromacs is that it comes with a large number of useful analysis tools that make many of the standard analysis tasks simple to perform ;NAMD/[[VMD]]: VMD can be used through its GUI or by scripting it in [[tcl]] to great effect ;[[Charmm]]: Charmm is feature-rich but its scripting language can cause a steep learning curve ;LAMMPS/[[pizza]]: pizza.py is a python library geared towards output from [[LAMMPS]] ;Amber/[[ptraj]]: command-line based analysis == MD Analysis libraries == ;[http://mdanalysis.googlecode.com/ MDAnalysis]: a python library to analyze dcd trajectories (in conjunction with a psf) ;[http://dirac.cnrs-orleans.fr/MMTK/ MMTK]: Another python-based framework for doing analysis is the ''Molecular Modelling Tool Kit''. However, it does not natively read [[Charmm]] dcd files and hence it can be cumbersome to use. ;[http://membrane.urmc.rochester.edu/Software/LOOS/Docs/main.html LOOS]: The ''Lightweight Object-Oriented Structure library (LOOS)'' from Alan Grossfield's lab provides a lightweight C++ library for analysis of molecular dynamics simulations. This includes parsing a number of PDB variants, as well as the native system description and trajectory formats for CHARMM, NAMD, and Amber. LOOS is not intended to be an all-encompassing library and it is primarily geared towards reading data in and processing rather than manipulating the files and structures and writing them out. == Specialized tools == ;[http://hole.biop.ox.ac.uk/hole HOLE]: Oliver Smart's program to trace out pore surfaces and estimate single channel conductances. ;CAVER: [http://loschmidt.chemi.muni.cz/caver/index.php CAVER] provides rapid, accurate and fully automated calculation of pathways leading from buried cavities to outside solvent in static and dynamic protein structures. Calculated pathways can be visualized by graphic program PyMol dissecting anatomy and dynamics of entrance tunnels. CAVER allows analysis of any molecular structure including proteins, nucleic acids, inorganic materials, etc. CAVER is available as [http://loschmidt.chemi.muni.cz/caver/online.php online version] or [[PyMol]] plugin suitable for calculation of pathways in discrete protein structures and stand alone version enabling analysis of trajectories from the molecular dynamics simulations. ;[http://swift.cmbi.ru.nl/gv/dssp/ dssp]: ''Definition of secondary structure of proteins given a set of 3D coordinates.'' The DSSP program defines secondary structure, geometrical features and solvent exposure of proteins, given atomic coordinates in Protein Data Bank format. The program does NOT PREDICT protein structure. According to the Science Citation Index (July 1995), the program has been cited in the scientific literature more than 1000 times. ; [http://www.compbio.dundee.ac.uk/manuals/stamp.4.2/stamp.html STAMP]: ''Structural Alignment of Multiple Proteins''. STAMP is a package for the alignment of protein sequence based on three-dimensional (3D) structure. It provides not only multiple alignments and the corresponding `best-fit' superimpositions, but also a systematic and reproducible method for assessing the quality of such alignments. It also provides a method for protein 3D structure data base scanning. In addition to structure comparison, the STAMP package provides input for programs to display and analyse protein sequence alignments and tertiary structures. Please note that, although STAMP outputs a sequence alignment, it is a program for 3D structures, and NOT sequences. ;[[swinker]]: finds and calculates helix hinges. It optionally finds the hinge point and calculates kink and swivel angles. == General purpose mathematical packages == ;[[Scientific Python]] and [[pylab]]: a [[matlab]]-like [[python]] module that has sophisticated analysis and plotting capabilities ;[[matlab]]: ;[[Mathematica]]: ;[[R]]: R is a language and environment for statistical computing and graphics. R provides a wide variety of statistical (linear and nonlinear modelling, classical statistical tests, time-series analysis, classification, clustering, ...) and graphical techniques, and is highly extensible. One of R's strengths is the ease with which well-designed publication-quality plots can be produced, including mathematical symbols and formulae where needed. Great care has been taken over the defaults for the minor design choices in graphics, but the user retains full control. [[Category:Analysis]] [[Category:Software]] b1fed782a105251917c6d4059beb6cf47916921a 227 218 2010-08-16T18:17:27Z Agrossfield 13 /* MD Analysis libraries -- updated link for LOOS to point to the distribution web page on sourceforge*/ wikitext text/x-wiki Running simulations is often the easy bit. The hard bit is to extract meaningful information from the Gigabytes of trajectory data. This list can act as a starting point. For most advanced uses, however, one will probably have to write analysis code in [[python]], [[Perl]], [[tcl]], [[C/C++]], [[bash]] ... or any other language that "gets the job done". == "Native" tools == Many of the [[Molecular dynamics software|MD packages]] come with their own analysis tools or scripting language. Sometimes it is possible to [[convert data formats]] between packages and use the other package's analysis tools. ;[[Gromacs]] analysis tools: oone of the strengths of Gromacs is that it comes with a large number of useful analysis tools that make many of the standard analysis tasks simple to perform ;NAMD/[[VMD]]: VMD can be used through its GUI or by scripting it in [[tcl]] to great effect ;[[Charmm]]: Charmm is feature-rich but its scripting language can cause a steep learning curve ;LAMMPS/[[pizza]]: pizza.py is a python library geared towards output from [[LAMMPS]] ;Amber/[[ptraj]]: command-line based analysis == MD Analysis libraries == ;[http://mdanalysis.googlecode.com/ MDAnalysis]: a python library to analyze dcd trajectories (in conjunction with a psf) ;[http://dirac.cnrs-orleans.fr/MMTK/ MMTK]: Another python-based framework for doing analysis is the ''Molecular Modelling Tool Kit''. However, it does not natively read [[Charmm]] dcd files and hence it can be cumbersome to use. ;[http://loos.sourceforge.net LOOS]: The ''Lightweight Object-Oriented Structure library (LOOS)'' from Alan Grossfield's lab provides a lightweight C++ library for analysis of molecular dynamics simulations. This includes parsing a number of PDB variants, as well as the native system description and trajectory formats for CHARMM, NAMD, and Amber. LOOS is not intended to be an all-encompassing library and it is primarily geared towards reading data in and processing rather than manipulating the files and structures and writing them out. == Specialized tools == ;[http://hole.biop.ox.ac.uk/hole HOLE]: Oliver Smart's program to trace out pore surfaces and estimate single channel conductances. ;CAVER: [http://loschmidt.chemi.muni.cz/caver/index.php CAVER] provides rapid, accurate and fully automated calculation of pathways leading from buried cavities to outside solvent in static and dynamic protein structures. Calculated pathways can be visualized by graphic program PyMol dissecting anatomy and dynamics of entrance tunnels. CAVER allows analysis of any molecular structure including proteins, nucleic acids, inorganic materials, etc. CAVER is available as [http://loschmidt.chemi.muni.cz/caver/online.php online version] or [[PyMol]] plugin suitable for calculation of pathways in discrete protein structures and stand alone version enabling analysis of trajectories from the molecular dynamics simulations. ;[http://swift.cmbi.ru.nl/gv/dssp/ dssp]: ''Definition of secondary structure of proteins given a set of 3D coordinates.'' The DSSP program defines secondary structure, geometrical features and solvent exposure of proteins, given atomic coordinates in Protein Data Bank format. The program does NOT PREDICT protein structure. According to the Science Citation Index (July 1995), the program has been cited in the scientific literature more than 1000 times. ; [http://www.compbio.dundee.ac.uk/manuals/stamp.4.2/stamp.html STAMP]: ''Structural Alignment of Multiple Proteins''. STAMP is a package for the alignment of protein sequence based on three-dimensional (3D) structure. It provides not only multiple alignments and the corresponding `best-fit' superimpositions, but also a systematic and reproducible method for assessing the quality of such alignments. It also provides a method for protein 3D structure data base scanning. In addition to structure comparison, the STAMP package provides input for programs to display and analyse protein sequence alignments and tertiary structures. Please note that, although STAMP outputs a sequence alignment, it is a program for 3D structures, and NOT sequences. ;[[swinker]]: finds and calculates helix hinges. It optionally finds the hinge point and calculates kink and swivel angles. == General purpose mathematical packages == ;[[Scientific Python]] and [[pylab]]: a [[matlab]]-like [[python]] module that has sophisticated analysis and plotting capabilities ;[[matlab]]: ;[[Mathematica]]: ;[[R]]: R is a language and environment for statistical computing and graphics. R provides a wide variety of statistical (linear and nonlinear modelling, classical statistical tests, time-series analysis, classification, clustering, ...) and graphical techniques, and is highly extensible. One of R's strengths is the ease with which well-designed publication-quality plots can be produced, including mathematical symbols and formulae where needed. Great care has been taken over the defaults for the minor design choices in graphics, but the user retains full control. [[Category:Analysis]] [[Category:Software]] 9fbee902b32b3ecd1a00d6d7fc97b2ca8738fd66 233 227 2011-04-21T01:08:19Z Oliver 2 /* MD Analysis libraries */ wikitext text/x-wiki Running simulations is often the easy bit. The hard bit is to extract meaningful information from the Gigabytes of trajectory data. This list can act as a starting point. For most advanced uses, however, one will probably have to write analysis code in [[python]], [[Perl]], [[tcl]], [[C/C++]], [[bash]] ... or any other language that "gets the job done". == "Native" tools == Many of the [[Molecular dynamics software|MD packages]] come with their own analysis tools or scripting language. Sometimes it is possible to [[convert data formats]] between packages and use the other package's analysis tools. ;[[Gromacs]] analysis tools: oone of the strengths of Gromacs is that it comes with a large number of useful analysis tools that make many of the standard analysis tasks simple to perform ;NAMD/[[VMD]]: VMD can be used through its GUI or by scripting it in [[tcl]] to great effect ;[[Charmm]]: Charmm is feature-rich but its scripting language can cause a steep learning curve ;LAMMPS/[[pizza]]: pizza.py is a python library geared towards output from [[LAMMPS]] ;Amber/[[ptraj]]: command-line based analysis == MD Analysis libraries == ;[http://mdanalysis.googlecode.com/ MDAnalysis]: a python library to analyze a range of trajectories (e.g. DCD, XTC, TRR, XYZ) and single frames (PDB, GRO, CRD, PQR). ;[http://dirac.cnrs-orleans.fr/MMTK/ MMTK]: Another python-based framework for doing analysis is the ''Molecular Modelling Tool Kit''. However, it does not natively read [[Charmm]] dcd files and hence it can be cumbersome to use. ;[http://loos.sourceforge.net LOOS]: The ''Lightweight Object-Oriented Structure library (LOOS)'' from Alan Grossfield's lab provides a lightweight C++ library for analysis of molecular dynamics simulations. This includes parsing a number of PDB variants, as well as the native system description and trajectory formats for CHARMM, NAMD, and Amber. LOOS is not intended to be an all-encompassing library and it is primarily geared towards reading data in and processing rather than manipulating the files and structures and writing them out. == Specialized tools == ;[http://hole.biop.ox.ac.uk/hole HOLE]: Oliver Smart's program to trace out pore surfaces and estimate single channel conductances. ;CAVER: [http://loschmidt.chemi.muni.cz/caver/index.php CAVER] provides rapid, accurate and fully automated calculation of pathways leading from buried cavities to outside solvent in static and dynamic protein structures. Calculated pathways can be visualized by graphic program PyMol dissecting anatomy and dynamics of entrance tunnels. CAVER allows analysis of any molecular structure including proteins, nucleic acids, inorganic materials, etc. CAVER is available as [http://loschmidt.chemi.muni.cz/caver/online.php online version] or [[PyMol]] plugin suitable for calculation of pathways in discrete protein structures and stand alone version enabling analysis of trajectories from the molecular dynamics simulations. ;[http://swift.cmbi.ru.nl/gv/dssp/ dssp]: ''Definition of secondary structure of proteins given a set of 3D coordinates.'' The DSSP program defines secondary structure, geometrical features and solvent exposure of proteins, given atomic coordinates in Protein Data Bank format. The program does NOT PREDICT protein structure. According to the Science Citation Index (July 1995), the program has been cited in the scientific literature more than 1000 times. ; [http://www.compbio.dundee.ac.uk/manuals/stamp.4.2/stamp.html STAMP]: ''Structural Alignment of Multiple Proteins''. STAMP is a package for the alignment of protein sequence based on three-dimensional (3D) structure. It provides not only multiple alignments and the corresponding `best-fit' superimpositions, but also a systematic and reproducible method for assessing the quality of such alignments. It also provides a method for protein 3D structure data base scanning. In addition to structure comparison, the STAMP package provides input for programs to display and analyse protein sequence alignments and tertiary structures. Please note that, although STAMP outputs a sequence alignment, it is a program for 3D structures, and NOT sequences. ;[[swinker]]: finds and calculates helix hinges. It optionally finds the hinge point and calculates kink and swivel angles. == General purpose mathematical packages == ;[[Scientific Python]] and [[pylab]]: a [[matlab]]-like [[python]] module that has sophisticated analysis and plotting capabilities ;[[matlab]]: ;[[Mathematica]]: ;[[R]]: R is a language and environment for statistical computing and graphics. R provides a wide variety of statistical (linear and nonlinear modelling, classical statistical tests, time-series analysis, classification, clustering, ...) and graphical techniques, and is highly extensible. One of R's strengths is the ease with which well-designed publication-quality plots can be produced, including mathematical symbols and formulae where needed. Great care has been taken over the defaults for the minor design choices in graphics, but the user retains full control. [[Category:Analysis]] [[Category:Software]] 7e4e33c8ff41130655af77f5f3734ae4210ef3f7 0 5 219 14 2010-01-10T13:39:51Z Oliver 2 /* Explicit lipids */ shameless plug: lipidbook wikitext text/x-wiki Simulations of proteins must also represent the environment faithfully (simulations in [[vacuum simulations|vacuum]] are ''not'' appropriate in most cases and really date back to the days when computer resources were severely limited). The environment of a protein consists of the [[solvent]] and, if it's a membrane protein, of the [[lipid bilayer]]. Here we discuss methods to represent the '''lipid membrane'''. == Explicit lipids == Parameters for lipids are often not distributed with the standard force field files but can be found on the [http://lipidbook.bioch.ox.ac.uk lipidbook] site. === All atom === All atom representations include heavy atoms and ''all'' hydrogens. See [[#United atom|united atom]] for the alternative. === United atom === A ''united atom'' representation combines carbons and aliphatic hydrogens into ''unified'' particles. == Implicit membrane == === Dielectric slab === === Statistical potential-based membrane === The membrane is parametrized based on the distribution of amino acids along the bilayer normal <cite>Ulmschneider2005</cite>. == References == <biblio> #Ulmschneider2005 pmid=15723347 </biblio> 985e4b55dfdab4f060d8acf99156ff5b96b7279c 220 219 2010-01-10T13:40:12Z Oliver 2 /* Explicit lipids */ wikitext text/x-wiki Simulations of proteins must also represent the environment faithfully (simulations in [[vacuum simulations|vacuum]] are ''not'' appropriate in most cases and really date back to the days when computer resources were severely limited). The environment of a protein consists of the [[solvent]] and, if it's a membrane protein, of the [[lipid bilayer]]. Here we discuss methods to represent the '''lipid membrane'''. == Explicit lipids == Force-field parameters for lipids are often not distributed with the standard force field files but can be found on the [http://lipidbook.bioch.ox.ac.uk lipidbook] site. === All atom === All atom representations include heavy atoms and ''all'' hydrogens. See [[#United atom|united atom]] for the alternative. === United atom === A ''united atom'' representation combines carbons and aliphatic hydrogens into ''unified'' particles. == Implicit membrane == === Dielectric slab === === Statistical potential-based membrane === The membrane is parametrized based on the distribution of amino acids along the bilayer normal <cite>Ulmschneider2005</cite>. == References == <biblio> #Ulmschneider2005 pmid=15723347 </biblio> 2897efb12bf7b19c2781fde4dae6d7535676321b 0 59 221 2010-05-22T09:58:16Z Oliver 2 methods for setting up membrane protein simulations wikitext text/x-wiki == Methods for setting up membrane protein simulations == Published methods: ; [http://wwwuser.gwdg.de/~ggroenh/membed.html g_membed]: Slowly growing a shrunken peptide into a bilayer. See ''g_membed: Efficient insertion of a membrane protein into an equilibrated lipid bilayer with minimal perturbation''. Maarten G. Wolf, Martin Hoefling, Camilo Aponte-Santamaría, Helmut Grubmüller, Gerrit Groenhof. J Comp Chem (2010). doi:[http://dx.doi.org/10.1002/jcc.21507 10.1002/jcc.21507] ; Tielemann's "shrinking an exploded bilayer": Scale all COM coordinates of lipids to increase space ("explode"), insert peptide, shrink via MD (see recent Tieleman review). ''Setting up and running molecular dynamics simulations of membrane proteins.'' Kandt C, Ash WL, Tieleman DP. Methods '''41''' (2007), 475-88. doi:[http://dx.doi.org/10.1016/j.ymeth.2006.08.006 10.1016/j.ymeth.2006.08.006] ; TaraGrid: an update on the Faraldo-Goméz/Smith "make hole" approach (?); ''Automated Protein-Insertion into Membranes for Molecular Dynamics Simulation Set-Up Using Taragrid'', René Staritzbichler, Lucy R. Forrest and José Faraldo-Gómez. Biophysics 2010 abstract [http://dx.doi.org/10.1016/j.bpj.2009.12.2105 10.1016/j.bpj.2009.12.2105] ; Griffin: Biophysics 2010 abstract ''Automated and Optimized Embedding of Proteins into Membranes for Molecular Dynamics Simulations using Griffin'', René Staritzbichler, Lucy R. Forresta and José D. Faraldo-Gómez doi:[http://dx.doi.org/10.1016/j.bpj.2009.12.3070 10.1016/j.bpj.2009.12.3070] ; gromacs make_hole: Faraldo-Goméz/Smith: use GRASP surface to gently generate a protein shaped hole in the bilayer; requires a special Gromacs binary [http://www.gromacs.org/@api/deki/files/48/=mdrun_make_hole.tar.gz mdrun_make_hole]. ''Setting up and optimization of membrane protein simulations.'' Faraldo-Gómez JD, Smith GR, Sansom MSP. Eur Biophys J. '''31'' (2002), 217-227. doi:[http://dx.doi.org/10.1007/s00249-002-0207-5 10.1007/s00249-002-0207-5] ; CHARMM style (Woolf & Roux): build bilayer from a library of lipid conformers+bound water that are translated and rotated as rigid units Files in the contributed section of CHARMM and at [http://thallium.bsd.uchicago.edu/RouxLab/membrane.html membrane builder]. ''Molecular dynamics simulation of the gramicidin channel in a phospholipid bilayer.'' Woolf TB, Roux B. Proc Natl Acad Sci U S A. '''91''' (1994), 11631-5 and ''Structure, energetics, and dynamics of lipid-protein interactions: A molecular dynamics study of the gramicidin A channel in a DMPC bilayer'', T. Woolf and B. Roux, Proteins '''24''' (1996) 92-114 doi:[http://www3.interscience.wiley.com/journal/69546/abstract 10.1002/(SICI)1097-0134(199601)24:1&lt;92::AID-PROT7&gt;3.0.CO;2-Q] ; CHARMM-GUI [http://www.charmm-gui.org/?doc=input/membrane Membrane-builder]: automated web procedure (generate input files, run locally. ''Automated Builder and Database of Protein/Membrane Complexes for Molecular Dynamics Simulations'', S. Jo, T. Kim, and W. Im PLoS ONE '''2''' (2007) e880 . [http://dx.doi.org/10.1371/journal.pone.0000880 10.1371/journal.pone.0000880]. [[Category:MembraneInsertion]] [[Category:Lipids]] [[Category:Protocols]] [[Category:Gromacs]] [[Category:CHARMM]] fdb2af5872d46372f22477d6a849e213e565e247 224 221 2010-05-22T10:13:24Z Oliver 2 overview wikitext text/x-wiki [[Category:Lipids]] [[Category:Protocols]] == Setting up membrane protein simulations == # decide on the [[Protein/Membrane system size|size of the protein/membrane system]] # obtain parameters (for lipids see, for instance, [http://lipidbook.bioch.ox.ac.uk Lipidbook]) # choose a [[transmembrane protein insertion methods|transmembrane protein insertion method]] # run simulation 73e359637511beda3f20f2e2d51caacf956be6bc 0 60 222 2010-05-22T10:11:49Z Oliver 2 estimate num ber of lipids (from SBCBWiki, written by OB) wikitext text/x-wiki This page collects notes on how to decide how to initially setup a membrane protein simulation. ''Please do not follow these notes blindly &mdash; they are more [http://www.imdb.com/title/tt0325980/quotes guidelines] than actual rules.'' Once you've decided on box dimensions and number of lipids you can use any of the [[Membrane protein insertion]] methods to set up the system. == System size == * Decide on the bilayer composition. Have you got [[Lipid FFDB|force field parameters for the lipids]]? * System size: ** rule of thumb 1: have at least 2-3 lipid layers between protein and periodic box boundary in the x-y plane to ensure(?) membrane-like behaviour; more may be necessary: you will need to monitor the hydrophobic mismatch and make the system big enough so that the bilayer at the box edges has its natural thickness. ** rule of thumb 2: have at least 1-1.5nm of water between protein and z-boundary (so that Coulomb forces are effectively screened) ** Especially for coarse-grained self-assembly simulations you also need to take into account the [[BONDINI#A rough guide to System Content and Membrane Structure|lipid-to-water ratio and its affect on membrane structure]]. * Add ions at eg 100 mM (+counter ions) for additional Coulomb screening * Remember that run time scales like <math>N \log N</math> (or even <math>N^2</math>) and <math>N</math> scales with the volume, i.e. <math>L^3</math>! Thus: keep your system small and pretty (ie the smallest system that still behaves like a big system... invariably you are trading size-artifacts versus speed and thus sampling) == Number of lipids == Estimate the cross sectional area of the protein, eg using the radius of gyration <math>A_{\mathrm{prot}} = \pi R_G</math> and with the approximate area per lipid <math>A_l = 64</math> Å the number of lipids in two leaflets is for a box with dimensions <math>L_x</math> and <math>L_y</math> <math>N = \frac{2(L_x L_y - A_\mathrm{prot})}{A_l}</math>. If you are simulating a mixed bilayer, eg POPE:POPG 4:1 then you will need <math>4N/5</math> POPE lipids and <math>N/5</math> POPG ones. == Number of ions == <!-- Oli Labbook p 42 --> Once the system is solvated you can calculate the numbers of ions <math>N</math> needed for a given concentration <math>c</math> (in addition to any counter ions): <math>c = \frac{n}{V} = \frac{N/N_A}{V}</math> (where <math>N_A = 6.02214179 \times 10^{23} \mathrm{mol}^{-1}</math> is the [http://physics.nist.gov/cgi-bin/cuu/Value?na Avogadro constant]). The problem is to get the water volume of the inhomogenous system, consisting of membrane and protein with the water. An approximation is to use the volume of a water molecule at standard conditions, <math>v_w = 30 \mathrm{\AA}^3</math> and calculate <math>V = N_w v_w</math> from the number of waters in the system, <math>N_w</math>. The equations become even simpler if we use the standard concentration of water, <math>c_w = n_w/(N_w v_w) = 55.5\, \mathrm{mol/l}</math>. Using all this we get <math>N_+ = \frac{c_+}{V} = \frac{c_+}{c_w} N_w</math> for the (monovalent) cations, and correspondingly for monovalent anions <math>N_- = N_+</math> === Example === For a concentration of 100 mM = 0.1 M and 8000 water molecules we will need to add <math>N_+ = N_- = \frac{0.1\,\mathrm{M}}{55.5\,\mathrm{M}} \times 8000 = 14</math> ions of each kind (eg 14 sodium and 14 chloride and whatever counterions are required to make the system charge neutral). [[Category:MembraneInsertion]] [[Category:Lipids]] [[Category:Tutorial]] 3a38aff56641ea05f6b1ba7f6eb654bc4752b17a 226 222 2010-05-22T10:28:02Z Oliver 2 math -> manual formatting wikitext text/x-wiki This page collects notes on how to decide how to initially setup a membrane protein simulation. ''Please do not follow these notes blindly &mdash; they are more [http://www.imdb.com/title/tt0325980/quotes guidelines] than actual rules.'' Once you've decided on box dimensions and number of lipids you can use any of the [[Transmembrane protein insertion methods]] methods to set up the system. == System size == * Decide on the bilayer composition. Have you got [[Lipid FFDB|force field parameters for the lipids]]? * System size: ** rule of thumb 1: have at least 2-3 lipid layers between protein and periodic box boundary in the x-y plane to ensure(?) membrane-like behaviour; more may be necessary: you will need to monitor the hydrophobic mismatch and make the system big enough so that the bilayer at the box edges has its natural thickness. ** rule of thumb 2: have at least 1-1.5nm of water between protein and z-boundary (so that Coulomb forces are effectively screened) ** Especially for coarse-grained self-assembly simulations you also need to take into account the [[BONDINI#A rough guide to System Content and Membrane Structure|lipid-to-water ratio and its affect on membrane structure]]. * Add ions at e.g. 100 mM (+counter ions) for additional Coulomb screening * Remember that run time scales like ''N'' log ''N'' (or even ''N''²) and ''N'' scales with the volume, i.e. ''L''³! Thus: keep your system small and pretty (i.e. the smallest system that still behaves like a big system... invariably you are trading size-artifacts versus speed and thus sampling) == Number of lipids == Estimate the cross sectional area of the protein, e.g. using the radius of gyration ''A''_prot = π ''R''_G and with the approximate area per lipid ''A''_l = 64 Å the number of lipids in two leaflets is for a box with dimensions ''L''_x and ''L''_y ''N'' = 2(''L''_x''L''_y - ''A''_prot) / ''A''_l If you are simulating a mixed bilayer, e.g. POPE:POPG 4:1 then you will need 4''N''/5 POPE lipids and ''N/''5 POPG ones. == Number of ions == Once the system is solvated you can calculate the numbers of ions <math>N</math> needed for a given concentration ''c'' (in addition to any counter ions): ''c'' = ''n''/''V'' = ''N''/(''N_AV) (where ''N''_A = 6.02214179 &times; 10²³mol^-1 is the [http://physics.nist.gov/cgi-bin/cuu/Value?na Avogadro constant]). The problem is to get the water volume of the inhomogenous system, consisting of membrane and protein with the water. An approximation is to use the volume of a water molecule at standard conditions, ''v''_w = 30 ų and calculate ''V'' = ''N''_w ''v''_w from the number of waters in the system, ''N''_w. The equations become even simpler if we use the standard concentration of water, ''c''_w = ''n''_w/(''N''_w ''v''_w) = 55.5 mol/l. Using all this we get N₊ = ''c''₊/''V'' = ''c''₊/''c''_w ''N''_w for the (monovalent) cations, and correspondingly for monovalent anions ''N''_- = ''N''₊ === Example === For a concentration of 100 mM = 0.1 M and 8000 water molecules we will need to add ''N''_- = ''N''₊ = 0.1 M/55.5 M &times; 8000 = 14 ions of each kind (e.g. 14 sodium and 14 chloride and whatever counterions are required to make the system charge neutral). [[Category:MembraneInsertion]] [[Category:Lipids]] [[Category:Tutorial]] e2f689c7580ed5cc6e9aabb6a9848254b19bf50c 0 61 223 2010-05-22T10:12:53Z Oliver 2 moved insertion methods to extra page wikitext text/x-wiki == Methods for setting up membrane protein simulations == Published methods: ; [http://wwwuser.gwdg.de/~ggroenh/membed.html g_membed]: Slowly growing a shrunken peptide into a bilayer. See ''g_membed: Efficient insertion of a membrane protein into an equilibrated lipid bilayer with minimal perturbation''. Maarten G. Wolf, Martin Hoefling, Camilo Aponte-Santamaría, Helmut Grubmüller, Gerrit Groenhof. J Comp Chem (2010). doi:[http://dx.doi.org/10.1002/jcc.21507 10.1002/jcc.21507] ; Tielemann's "shrinking an exploded bilayer": Scale all COM coordinates of lipids to increase space ("explode"), insert peptide, shrink via MD (see recent Tieleman review). ''Setting up and running molecular dynamics simulations of membrane proteins.'' Kandt C, Ash WL, Tieleman DP. Methods '''41''' (2007), 475-88. doi:[http://dx.doi.org/10.1016/j.ymeth.2006.08.006 10.1016/j.ymeth.2006.08.006] ; TaraGrid: an update on the Faraldo-Goméz/Smith "make hole" approach (?); ''Automated Protein-Insertion into Membranes for Molecular Dynamics Simulation Set-Up Using Taragrid'', René Staritzbichler, Lucy R. Forrest and José Faraldo-Gómez. Biophysics 2010 abstract [http://dx.doi.org/10.1016/j.bpj.2009.12.2105 10.1016/j.bpj.2009.12.2105] ; Griffin: Biophysics 2010 abstract ''Automated and Optimized Embedding of Proteins into Membranes for Molecular Dynamics Simulations using Griffin'', René Staritzbichler, Lucy R. Forresta and José D. Faraldo-Gómez doi:[http://dx.doi.org/10.1016/j.bpj.2009.12.3070 10.1016/j.bpj.2009.12.3070] ; gromacs make_hole: Faraldo-Goméz/Smith: use GRASP surface to gently generate a protein shaped hole in the bilayer; requires a special Gromacs binary [http://www.gromacs.org/@api/deki/files/48/=mdrun_make_hole.tar.gz mdrun_make_hole]. ''Setting up and optimization of membrane protein simulations.'' Faraldo-Gómez JD, Smith GR, Sansom MSP. Eur Biophys J. '''31'' (2002), 217-227. doi:[http://dx.doi.org/10.1007/s00249-002-0207-5 10.1007/s00249-002-0207-5] ; CHARMM style (Woolf & Roux): build bilayer from a library of lipid conformers+bound water that are translated and rotated as rigid units Files in the contributed section of CHARMM and at [http://thallium.bsd.uchicago.edu/RouxLab/membrane.html membrane builder]. ''Molecular dynamics simulation of the gramicidin channel in a phospholipid bilayer.'' Woolf TB, Roux B. Proc Natl Acad Sci U S A. '''91''' (1994), 11631-5 and ''Structure, energetics, and dynamics of lipid-protein interactions: A molecular dynamics study of the gramicidin A channel in a DMPC bilayer'', T. Woolf and B. Roux, Proteins '''24''' (1996) 92-114 doi:[http://www3.interscience.wiley.com/journal/69546/abstract 10.1002/(SICI)1097-0134(199601)24:1&lt;92::AID-PROT7&gt;3.0.CO;2-Q] ; CHARMM-GUI [http://www.charmm-gui.org/?doc=input/membrane Membrane-builder]: automated web procedure (generate input files, run locally. ''Automated Builder and Database of Protein/Membrane Complexes for Molecular Dynamics Simulations'', S. Jo, T. Kim, and W. Im PLoS ONE '''2''' (2007) e880 . [http://dx.doi.org/10.1371/journal.pone.0000880 10.1371/journal.pone.0000880]. [[Category:MembraneInsertion]] [[Category:Lipids]] [[Category:Protocols]] [[Category:Gromacs]] [[Category:CHARMM]] fdb2af5872d46372f22477d6a849e213e565e247 225 223 2010-05-22T10:15:03Z Oliver 2 wikitext text/x-wiki Published methods for setting up membrane protein simulations; please add more. ; [http://wwwuser.gwdg.de/~ggroenh/membed.html g_membed]: Slowly growing a shrunken peptide into a bilayer. See ''g_membed: Efficient insertion of a membrane protein into an equilibrated lipid bilayer with minimal perturbation''. Maarten G. Wolf, Martin Hoefling, Camilo Aponte-Santamaría, Helmut Grubmüller, Gerrit Groenhof. J Comp Chem (2010). doi:[http://dx.doi.org/10.1002/jcc.21507 10.1002/jcc.21507] ; Tielemann's "shrinking an exploded bilayer": Scale all COM coordinates of lipids to increase space ("explode"), insert peptide, shrink via MD (see recent Tieleman review). ''Setting up and running molecular dynamics simulations of membrane proteins.'' Kandt C, Ash WL, Tieleman DP. Methods '''41''' (2007), 475-88. doi:[http://dx.doi.org/10.1016/j.ymeth.2006.08.006 10.1016/j.ymeth.2006.08.006] ; TaraGrid: an update on the Faraldo-Goméz/Smith "make hole" approach (?); ''Automated Protein-Insertion into Membranes for Molecular Dynamics Simulation Set-Up Using Taragrid'', René Staritzbichler, Lucy R. Forrest and José Faraldo-Gómez. Biophysics 2010 abstract [http://dx.doi.org/10.1016/j.bpj.2009.12.2105 10.1016/j.bpj.2009.12.2105] ; Griffin: Biophysics 2010 abstract ''Automated and Optimized Embedding of Proteins into Membranes for Molecular Dynamics Simulations using Griffin'', René Staritzbichler, Lucy R. Forresta and José D. Faraldo-Gómez doi:[http://dx.doi.org/10.1016/j.bpj.2009.12.3070 10.1016/j.bpj.2009.12.3070] ; gromacs make_hole: Faraldo-Goméz/Smith: use GRASP surface to gently generate a protein shaped hole in the bilayer; requires a special Gromacs binary [http://www.gromacs.org/@api/deki/files/48/=mdrun_make_hole.tar.gz mdrun_make_hole]. ''Setting up and optimization of membrane protein simulations.'' Faraldo-Gómez JD, Smith GR, Sansom MSP. Eur Biophys J. '''31'' (2002), 217-227. doi:[http://dx.doi.org/10.1007/s00249-002-0207-5 10.1007/s00249-002-0207-5] ; CHARMM style (Woolf & Roux): build bilayer from a library of lipid conformers+bound water that are translated and rotated as rigid units Files in the contributed section of CHARMM and at [http://thallium.bsd.uchicago.edu/RouxLab/membrane.html membrane builder]. ''Molecular dynamics simulation of the gramicidin channel in a phospholipid bilayer.'' Woolf TB, Roux B. Proc Natl Acad Sci U S A. '''91''' (1994), 11631-5 and ''Structure, energetics, and dynamics of lipid-protein interactions: A molecular dynamics study of the gramicidin A channel in a DMPC bilayer'', T. Woolf and B. Roux, Proteins '''24''' (1996) 92-114 doi:[http://www3.interscience.wiley.com/journal/69546/abstract 10.1002/(SICI)1097-0134(199601)24:1&lt;92::AID-PROT7&gt;3.0.CO;2-Q] ; CHARMM-GUI [http://www.charmm-gui.org/?doc=input/membrane Membrane-builder]: automated web procedure (generate input files, run locally. ''Automated Builder and Database of Protein/Membrane Complexes for Molecular Dynamics Simulations'', S. Jo, T. Kim, and W. Im PLoS ONE '''2''' (2007) e880 . [http://dx.doi.org/10.1371/journal.pone.0000880 10.1371/journal.pone.0000880]. [[Category:MembraneInsertion]] [[Category:Lipids]] [[Category:Protocols]] [[Category:Gromacs]] [[Category:CHARMM]] 762ac60998ed08c5cfbd0da8a4b1fc0e80bb5db6 228 225 2010-10-12T07:10:54Z Renedominik 15 wikitext text/x-wiki Published methods for setting up membrane protein simulations; please add more. ; [http://wwwuser.gwdg.de/~ggroenh/membed.html g_membed]: Slowly growing a shrunken peptide into a bilayer. See ''g_membed: Efficient insertion of a membrane protein into an equilibrated lipid bilayer with minimal perturbation''. Maarten G. Wolf, Martin Hoefling, Camilo Aponte-Santamaría, Helmut Grubmüller, Gerrit Groenhof. J Comp Chem (2010). doi:[http://dx.doi.org/10.1002/jcc.21507 10.1002/jcc.21507] ; Tielemann's "shrinking an exploded bilayer": Scale all COM coordinates of lipids to increase space ("explode"), insert peptide, shrink via MD (see recent Tieleman review). ''Setting up and running molecular dynamics simulations of membrane proteins.'' Kandt C, Ash WL, Tieleman DP. Methods '''41''' (2007), 475-88. doi:[http://dx.doi.org/10.1016/j.ymeth.2006.08.006 10.1016/j.ymeth.2006.08.006] ; Griffin: Biophysics 2010 abstract ''Automated and Optimized Embedding of Proteins into Membranes for Molecular Dynamics Simulations using Griffin'', René Staritzbichler, Lucy R. Forresta and José D. Faraldo-Gómez doi:[http://dx.doi.org/10.1016/j.bpj.2009.12.3070 10.1016/j.bpj.2009.12.3070] ; gromacs make_hole: Faraldo-Goméz/Smith: use GRASP surface to gently generate a protein shaped hole in the bilayer; requires a special Gromacs binary [http://www.gromacs.org/@api/deki/files/48/=mdrun_make_hole.tar.gz mdrun_make_hole]. ''Setting up and optimization of membrane protein simulations.'' Faraldo-Gómez JD, Smith GR, Sansom MSP. Eur Biophys J. '''31'' (2002), 217-227. doi:[http://dx.doi.org/10.1007/s00249-002-0207-5 10.1007/s00249-002-0207-5] ; CHARMM style (Woolf & Roux): build bilayer from a library of lipid conformers+bound water that are translated and rotated as rigid units Files in the contributed section of CHARMM and at [http://thallium.bsd.uchicago.edu/RouxLab/membrane.html membrane builder]. ''Molecular dynamics simulation of the gramicidin channel in a phospholipid bilayer.'' Woolf TB, Roux B. Proc Natl Acad Sci U S A. '''91''' (1994), 11631-5 and ''Structure, energetics, and dynamics of lipid-protein interactions: A molecular dynamics study of the gramicidin A channel in a DMPC bilayer'', T. Woolf and B. Roux, Proteins '''24''' (1996) 92-114 doi:[http://www3.interscience.wiley.com/journal/69546/abstract 10.1002/(SICI)1097-0134(199601)24:1&lt;92::AID-PROT7&gt;3.0.CO;2-Q] ; CHARMM-GUI [http://www.charmm-gui.org/?doc=input/membrane Membrane-builder]: automated web procedure (generate input files, run locally. ''Automated Builder and Database of Protein/Membrane Complexes for Molecular Dynamics Simulations'', S. Jo, T. Kim, and W. Im PLoS ONE '''2''' (2007) e880 . [http://dx.doi.org/10.1371/journal.pone.0000880 10.1371/journal.pone.0000880]. [[Category:MembraneInsertion]] [[Category:Lipids]] [[Category:Protocols]] [[Category:Gromacs]] [[Category:CHARMM]] 8edf796082765a65ab1eb68f86118c5a08f35a41 229 228 2010-10-12T07:11:26Z Renedominik 15 wikitext text/x-wiki Published methods for setting up membrane protein simulations; please add more. ; [http://wwwuser.gwdg.de/~ggroenh/membed.html g_membed]: Slowly growing a shrunken peptide into a bilayer. See ''g_membed: Efficient insertion of a membrane protein into an equilibrated lipid bilayer with minimal perturbation''. Maarten G. Wolf, Martin Hoefling, Camilo Aponte-Santamaría, Helmut Grubmüller, Gerrit Groenhof. J Comp Chem (2010). doi:[http://dx.doi.org/10.1002/jcc.21507 10.1002/jcc.21507] ; Tielemann's "shrinking an exploded bilayer": Scale all COM coordinates of lipids to increase space ("explode"), insert peptide, shrink via MD (see recent Tieleman review). ''Setting up and running molecular dynamics simulations of membrane proteins.'' Kandt C, Ash WL, Tieleman DP. Methods '''41''' (2007), 475-88. doi:[http://dx.doi.org/10.1016/j.ymeth.2006.08.006 10.1016/j.ymeth.2006.08.006] ; Griffin: Biophysics 2010 abstract ''Automated and Optimized Embedding of Proteins into Membranes for Molecular Dynamics Simulations using Griffin'', René Staritzbichler, Lucy R. Forrest and José D. Faraldo-Gómez doi:[http://dx.doi.org/10.1016/j.bpj.2009.12.3070 10.1016/j.bpj.2009.12.3070] ; gromacs make_hole: Faraldo-Goméz/Smith: use GRASP surface to gently generate a protein shaped hole in the bilayer; requires a special Gromacs binary [http://www.gromacs.org/@api/deki/files/48/=mdrun_make_hole.tar.gz mdrun_make_hole]. ''Setting up and optimization of membrane protein simulations.'' Faraldo-Gómez JD, Smith GR, Sansom MSP. Eur Biophys J. '''31'' (2002), 217-227. doi:[http://dx.doi.org/10.1007/s00249-002-0207-5 10.1007/s00249-002-0207-5] ; CHARMM style (Woolf & Roux): build bilayer from a library of lipid conformers+bound water that are translated and rotated as rigid units Files in the contributed section of CHARMM and at [http://thallium.bsd.uchicago.edu/RouxLab/membrane.html membrane builder]. ''Molecular dynamics simulation of the gramicidin channel in a phospholipid bilayer.'' Woolf TB, Roux B. Proc Natl Acad Sci U S A. '''91''' (1994), 11631-5 and ''Structure, energetics, and dynamics of lipid-protein interactions: A molecular dynamics study of the gramicidin A channel in a DMPC bilayer'', T. Woolf and B. Roux, Proteins '''24''' (1996) 92-114 doi:[http://www3.interscience.wiley.com/journal/69546/abstract 10.1002/(SICI)1097-0134(199601)24:1&lt;92::AID-PROT7&gt;3.0.CO;2-Q] ; CHARMM-GUI [http://www.charmm-gui.org/?doc=input/membrane Membrane-builder]: automated web procedure (generate input files, run locally. ''Automated Builder and Database of Protein/Membrane Complexes for Molecular Dynamics Simulations'', S. Jo, T. Kim, and W. Im PLoS ONE '''2''' (2007) e880 . [http://dx.doi.org/10.1371/journal.pone.0000880 10.1371/journal.pone.0000880]. [[Category:MembraneInsertion]] [[Category:Lipids]] [[Category:Protocols]] [[Category:Gromacs]] [[Category:CHARMM]] bb31774a3984aaded802e3d68e2e8d51ccb1858e 230 229 2010-10-12T14:02:35Z Renedominik 15 wikitext text/x-wiki Published methods for setting up membrane protein simulations; please add more. ; [http://wwwuser.gwdg.de/~ggroenh/membed.html g_membed]: Slowly growing a shrunken peptide into a bilayer. See ''g_membed: Efficient insertion of a membrane protein into an equilibrated lipid bilayer with minimal perturbation''. Maarten G. Wolf, Martin Hoefling, Camilo Aponte-Santamaría, Helmut Grubmüller, Gerrit Groenhof. J Comp Chem (2010). doi:[http://dx.doi.org/10.1002/jcc.21507 10.1002/jcc.21507] ; Tielemann's "shrinking an exploded bilayer": Scale all COM coordinates of lipids to increase space ("explode"), insert peptide, shrink via MD (see recent Tieleman review). ''Setting up and running molecular dynamics simulations of membrane proteins.'' Kandt C, Ash WL, Tieleman DP. Methods '''41''' (2007), 475-88. doi:[http://dx.doi.org/10.1016/j.ymeth.2006.08.006 10.1016/j.ymeth.2006.08.006] ; GRIFFIN: Biophysics 2010 abstract ''Automated and Optimized Embedding of Proteins into Membranes for Molecular Dynamics Simulations using GRIFFIN'', René Staritzbichler, Lucy R. Forrest and José D. Faraldo-Gómez doi:[http://dx.doi.org/10.1016/j.bpj.2009.12.3070 10.1016/j.bpj.2009.12.3070] ; gromacs make_hole: The predecessor of GRIFFIN (part of the Gromacs 3.1 version). Use GRASP surface to gently generate a protein shaped hole in the bilayer; requires a special Gromacs binary [http://www.gromacs.org/@api/deki/files/48/=mdrun_make_hole.tar.gz mdrun_make_hole]. ''Setting up and optimization of membrane protein simulations.'' Faraldo-Gómez JD, Smith GR, Sansom MSP. Eur Biophys J. '''31'' (2002), 217-227. doi:[http://dx.doi.org/10.1007/s00249-002-0207-5 10.1007/s00249-002-0207-5] ; CHARMM style (Woolf & Roux): build bilayer from a library of lipid conformers+bound water that are translated and rotated as rigid units Files in the contributed section of CHARMM and at [http://thallium.bsd.uchicago.edu/RouxLab/membrane.html membrane builder]. ''Molecular dynamics simulation of the gramicidin channel in a phospholipid bilayer.'' Woolf TB, Roux B. Proc Natl Acad Sci U S A. '''91''' (1994), 11631-5 and ''Structure, energetics, and dynamics of lipid-protein interactions: A molecular dynamics study of the gramicidin A channel in a DMPC bilayer'', T. Woolf and B. Roux, Proteins '''24''' (1996) 92-114 doi:[http://www3.interscience.wiley.com/journal/69546/abstract 10.1002/(SICI)1097-0134(199601)24:1&lt;92::AID-PROT7&gt;3.0.CO;2-Q] ; CHARMM-GUI [http://www.charmm-gui.org/?doc=input/membrane Membrane-builder]: automated web procedure (generate input files, run locally. ''Automated Builder and Database of Protein/Membrane Complexes for Molecular Dynamics Simulations'', S. Jo, T. Kim, and W. Im PLoS ONE '''2''' (2007) e880 . [http://dx.doi.org/10.1371/journal.pone.0000880 10.1371/journal.pone.0000880]. [[Category:MembraneInsertion]] [[Category:Lipids]] [[Category:Protocols]] [[Category:Gromacs]] [[Category:CHARMM]] 7efbf0d0d5e1c80ffd86d4276891d5ed085a18ba 231 230 2010-10-12T14:03:50Z Renedominik 15 wikitext text/x-wiki Published methods for setting up membrane protein simulations; please add more. ; [http://wwwuser.gwdg.de/~ggroenh/membed.html g_membed]: Slowly growing a shrunken peptide into a bilayer. See ''g_membed: Efficient insertion of a membrane protein into an equilibrated lipid bilayer with minimal perturbation''. Maarten G. Wolf, Martin Hoefling, Camilo Aponte-Santamaría, Helmut Grubmüller, Gerrit Groenhof. J Comp Chem (2010). doi:[http://dx.doi.org/10.1002/jcc.21507 10.1002/jcc.21507] ; Tielemann's "shrinking an exploded bilayer": Scale all COM coordinates of lipids to increase space ("explode"), insert peptide, shrink via MD (see recent Tieleman review). ''Setting up and running molecular dynamics simulations of membrane proteins.'' Kandt C, Ash WL, Tieleman DP. Methods '''41''' (2007), 475-88. doi:[http://dx.doi.org/10.1016/j.ymeth.2006.08.006 10.1016/j.ymeth.2006.08.006] ; GRIFFIN: Biophysics 2010 abstract ''Automated and Optimized Embedding of Proteins into Membranes for Molecular Dynamics Simulations using GRIFFIN'', René Staritzbichler, Lucy R. Forrest and José D. Faraldo-Gómez doi:[http://dx.doi.org/10.1016/j.bpj.2009.12.3070 10.1016/j.bpj.2009.12.3070] ; gromacs make_hole: The predecessor of GRIFFIN (part of Gromacs 3.1). Use GRASP surface to gently generate a protein shaped hole in the bilayer; requires a special Gromacs binary [http://www.gromacs.org/@api/deki/files/48/=mdrun_make_hole.tar.gz mdrun_make_hole]. ''Setting up and optimization of membrane protein simulations.'' Faraldo-Gómez JD, Smith GR, Sansom MSP. Eur Biophys J. '''31'' (2002), 217-227. doi:[http://dx.doi.org/10.1007/s00249-002-0207-5 10.1007/s00249-002-0207-5] ; CHARMM style (Woolf & Roux): build bilayer from a library of lipid conformers+bound water that are translated and rotated as rigid units Files in the contributed section of CHARMM and at [http://thallium.bsd.uchicago.edu/RouxLab/membrane.html membrane builder]. ''Molecular dynamics simulation of the gramicidin channel in a phospholipid bilayer.'' Woolf TB, Roux B. Proc Natl Acad Sci U S A. '''91''' (1994), 11631-5 and ''Structure, energetics, and dynamics of lipid-protein interactions: A molecular dynamics study of the gramicidin A channel in a DMPC bilayer'', T. Woolf and B. Roux, Proteins '''24''' (1996) 92-114 doi:[http://www3.interscience.wiley.com/journal/69546/abstract 10.1002/(SICI)1097-0134(199601)24:1&lt;92::AID-PROT7&gt;3.0.CO;2-Q] ; CHARMM-GUI [http://www.charmm-gui.org/?doc=input/membrane Membrane-builder]: automated web procedure (generate input files, run locally. ''Automated Builder and Database of Protein/Membrane Complexes for Molecular Dynamics Simulations'', S. Jo, T. Kim, and W. Im PLoS ONE '''2''' (2007) e880 . [http://dx.doi.org/10.1371/journal.pone.0000880 10.1371/journal.pone.0000880]. [[Category:MembraneInsertion]] [[Category:Lipids]] [[Category:Protocols]] [[Category:Gromacs]] [[Category:CHARMM]] 330926335ec4dfffcdb1396d4d8d2ea74b1c3fab 232 231 2010-10-12T15:32:51Z Renedominik 15 wikitext text/x-wiki Published methods for setting up membrane protein simulations; please add more. ; [http://wwwuser.gwdg.de/~ggroenh/membed.html g_membed]: Slowly growing a shrunken peptide into a bilayer. See ''g_membed: Efficient insertion of a membrane protein into an equilibrated lipid bilayer with minimal perturbation''. Maarten G. Wolf, Martin Hoefling, Camilo Aponte-Santamaría, Helmut Grubmüller, Gerrit Groenhof. J Comp Chem (2010). doi:[http://dx.doi.org/10.1002/jcc.21507 10.1002/jcc.21507] ; Tielemann's "shrinking an exploded bilayer": Scale all COM coordinates of lipids to increase space ("explode"), insert peptide, shrink via MD (see recent Tieleman review). ''Setting up and running molecular dynamics simulations of membrane proteins.'' Kandt C, Ash WL, Tieleman DP. Methods '''41''' (2007), 475-88. doi:[http://dx.doi.org/10.1016/j.ymeth.2006.08.006 10.1016/j.ymeth.2006.08.006] ; GRIFFIN: Calculates realistic lipid conformations even for large TM protein systems with complex topology starting from a pre-equilibrated bilayer. The implicit force field of GRIFFIN guides buried bilayer atoms towards the surface of the protein, while water or lipid atoms outside of the protein volume experience the interaction forces of the protein. Biophysics 2010 abstract ''Automated and Optimized Embedding of Proteins into Membranes for Molecular Dynamics Simulations using GRIFFIN'', René Staritzbichler, Lucy R. Forrest and José D. Faraldo-Gómez doi:[http://dx.doi.org/10.1016/j.bpj.2009.12.3070 10.1016/j.bpj.2009.12.3070] ; gromacs make_hole: The predecessor of GRIFFIN (part of Gromacs 3.1). Use GRASP surface to gently generate a protein shaped hole in the bilayer; requires a special Gromacs binary [http://www.gromacs.org/@api/deki/files/48/=mdrun_make_hole.tar.gz mdrun_make_hole]. ''Setting up and optimization of membrane protein simulations.'' Faraldo-Gómez JD, Smith GR, Sansom MSP. Eur Biophys J. '''31'' (2002), 217-227. doi:[http://dx.doi.org/10.1007/s00249-002-0207-5 10.1007/s00249-002-0207-5] ; CHARMM style (Woolf & Roux): build bilayer from a library of lipid conformers+bound water that are translated and rotated as rigid units Files in the contributed section of CHARMM and at [http://thallium.bsd.uchicago.edu/RouxLab/membrane.html membrane builder]. ''Molecular dynamics simulation of the gramicidin channel in a phospholipid bilayer.'' Woolf TB, Roux B. Proc Natl Acad Sci U S A. '''91''' (1994), 11631-5 and ''Structure, energetics, and dynamics of lipid-protein interactions: A molecular dynamics study of the gramicidin A channel in a DMPC bilayer'', T. Woolf and B. Roux, Proteins '''24''' (1996) 92-114 doi:[http://www3.interscience.wiley.com/journal/69546/abstract 10.1002/(SICI)1097-0134(199601)24:1&lt;92::AID-PROT7&gt;3.0.CO;2-Q] ; CHARMM-GUI [http://www.charmm-gui.org/?doc=input/membrane Membrane-builder]: automated web procedure (generate input files, run locally. ''Automated Builder and Database of Protein/Membrane Complexes for Molecular Dynamics Simulations'', S. Jo, T. Kim, and W. Im PLoS ONE '''2''' (2007) e880 . [http://dx.doi.org/10.1371/journal.pone.0000880 10.1371/journal.pone.0000880]. [[Category:MembraneInsertion]] [[Category:Lipids]] [[Category:Protocols]] [[Category:Gromacs]] [[Category:CHARMM]] 70eeeb254c72f1f50370b1d3a8fdb63150505698 2 62 236 2024-07-21T12:12:34Z PeteKaufman909 16 Created page with "53 year-old Telecommunications Technical Official or Technologist Harrold from Port McNicoll, has lots of passions which include wall art, camlock and camping. In recent years has made a journey to Longobards in Italy. Places of the Power (- A.D.).<br><br>Also visit my blog [https://www.castermetal.com/sand-casting-products-and-services/ what is it worth]" wikitext text/x-wiki 53 year-old Telecommunications Technical Official or Technologist Harrold from Port McNicoll, has lots of passions which include wall art, camlock and camping. In recent years has made a journey to Longobards in Italy. Places of the Power (- A.D.).<br><br>Also visit my blog [https://www.castermetal.com/sand-casting-products-and-services/ what is it worth] df9f78d92489f993a1d6557b7c5dc4ee12eb85d0 0 63 237 2024-07-21T12:12:40Z PeteKaufman909 16 Created page with "<br>Carbon steel induction cookware is one of the best investments for your home. It's affordable, durable, and a non-stick frying pan that cooks evenly and safely. The cast iron construction keeps food from sticking and creates a non-stick surface. This product is designed for all types of cooking, from regular frying to baking to broiling.<br><br><br>The Teflon coated non-stick surface reduces stickiness and prevents food from sticking. This frying pan is also a good c..." wikitext text/x-wiki <br>Carbon steel induction cookware is one of the best investments for your home. It's affordable, durable, and a non-stick frying pan that cooks evenly and safely. The cast iron construction keeps food from sticking and creates a non-stick surface. This product is designed for all types of cooking, from regular frying to baking to broiling.<br><br><br>The Teflon coated non-stick surface reduces stickiness and prevents food from sticking. This frying pan is also a good choice for quick, small orders. The cast iron body spreads heat evenly across the pan for consistently even cooking results. The Teflon coating on the handle and sides helps prevent foods from sticking and absorbs extra moisture for faster browning.<br><br><br>Some pans have built-in racks for items like beans, potatoes, or shrimp. Other owners may choose not to use racks because they are impatient while preparing their meals or because they want to control the spillage of melted oil. Some carbon steel cookware users say that the cast-iron pan interferes with their rhythm while preparing their meals. The Teflon coated handles and sides help prevent spillage and browning.<br><br><br>One unique feature is the cast aluminum handle, which is dishwasher safe and easy to grip. Many users say it's difficult to hold on to the cast aluminum handle with the thin metal handles of other woks. A one-handed twist makes carrying the pan easier. The lifetime warranty covers damages due to rust and breaks due to heavy use and excessive heat.<br><br><br>The Teflon coated steel makes it easier to clean up. If you cherished this short article and you would like to obtain more details about [https://www.castermetal.com/sand-casting-products-and-services/ link] kindly stop by our own web site. Carbon steel woks are also more durable than aluminum pans, making them ideal for a wide variety of cuisines. The handles and sides will remain cool even when hot, so you can safely bring them in the microwave without worry of it burning your hands.<br><br><br>One thing users say is most appreciated is the quick release latch that locks the lid tight without damaging it. No more poking yourself with a stick trying to loosen it! This lid also comes with a lifetime warranty, so there is no need to worry about spending money on repairs. Some owners prefer the flat bottom design because it allows for easier cleaning and doesn't interfere with the pan's bottom surface.<br><br><br>The Teflon coated steel has been certified by Underwriter's Laboratory as having an excellent balance of heat and non-heat. The Teflon coating ensures that food doesn't stick to the sides of the pan, which makes clean up much easier. It is not a true induction cooker, but users say the induction element is very gentle on the bottom and sides of the food. A carbon steel pan with a flat bottom is very traditional and adds a touch of traditional Asian flare to your kitchen. Many customers say this type of pan feels great on the stovetop as well. The flat bottom is easy to remove so it makes cleanup time faster and easier.<br><br><br>If you are looking for a sturdy pan with a non-stick coating that will keep your food from sticking, look no further than a Teflon coated steel non-stick pan with a stainless steel edge and snap-on lid for an affordable, yet high quality induction ready cookware. This cookware is perfect for induction heating. 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Some users replace their carbon steel pan handles as often as every couple of months.<br><br><br>There are many more advantages to using induction-ready pans. The Teflon coating protects the user's hands from burns when handling hot surfaces. The cast iron construction makes these fans ideal for induction heating. The stainless steel construction prevents rust from forming. And because these pans come in a variety of sizes, the user can choose the right size pan for their needs. With all these benefits, carbon steel pans are an excellent choice for induction-ready cookware.<br> eca77460db12dcad7bed055a61981fc44bec8492 2 64 238 2024-07-21T13:37:12Z NSXCarmon540145 17 Created page with "26 year-old Structural Analysis Engineer Deeanne Royds, hailing from Kelowna enjoys watching movies like Blood River and Soapmaking. Took a trip to Quseir Amra and drives a 3500 Club Coupe.<br><br>Feel free to visit my web blog [https://www.ilbaby.com/what-you-can-get-from-having-reborn-baby-dolls/ Reborn Baby]" wikitext text/x-wiki 26 year-old Structural Analysis Engineer Deeanne Royds, hailing from Kelowna enjoys watching movies like Blood River and Soapmaking. Took a trip to Quseir Amra and drives a 3500 Club Coupe.<br><br>Feel free to visit my web blog [https://www.ilbaby.com/what-you-can-get-from-having-reborn-baby-dolls/ Reborn Baby] d6a022817a214e3348acf9c5a93928784658d3ff 0 65 239 2024-07-21T13:37:17Z NSXCarmon540145 17 Created page with "<br>Full body silicone reborn baby dolls are a great way to create your very own lifelike doll. These miniature babies are alive and will respond to touch, heartbeat, and breathing. Even the first steps of your baby can be simulated. These realistic toys are also known for their lifelike resemblance to your own child. 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A diaphragm expansion tank, is made up of a little bottle, concerning the magnitude of a barbecue grill propane tank. <br> Ideas, Formulas and Shortcuts for 50mm Stainless Steel Pipe Price <br>The warranty demands professional installation. It is the sole warranty in this way in the business. Reliable manufacturers offer ample windows for optimal ventilation in addition to eco-friendly plumbing. Most significantly, the item is flexible and has a very simple installation procedure, in contrast to copper pipes. It's limited for the DIY market because it's just for expert installation. You may shape it to take whole benefit of every cubic inch and give maximum draft. So it's a good alternative for homeowners that are looking for handrails on a budget. <br><br><br>The maximum risk for pipes freezing lies in areas of the basement which are not properly insulated. Safety is no longer a matter here, as stone handrails offer high way of security. 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So, to give Prosecco gifts as gifts, why not check out some of the best cheap unlocking c..." wikitext text/x-wiki <br>Prosecco is a grape that grows in the Mediterranean climate and is known for its flavor. For this reason, it's often compared to champagne. However, what's most important about this sparkling wine is that it is also excellent when it comes to inexpensive, cheap gift items. Whether you're looking for cheap gifts for men or women, Prosecco would definitely be useful and enjoyable. So, to give Prosecco gifts as gifts, why not check out some of the best cheap unlocking cell phones and other cheap gifts available on the internet?<br> <br><br>There are actually several cheap unlocking mobile phone options on the market. Most notably, there are several unlocked disposable cell phones available for you to buy at cheap prices. As these cheap phones are made available in the market, they are usually unlocked. 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